Genetic Variant C19orf38:c.340+30G>A (chr19-10850597-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001136482.3(C19orf38):c.340+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,547,716 control chromosomes in the GnomAD database, including 114,990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10235 hom., cov: 31)

Exomes 𝑓: 0.39 ( 104755 hom. )

Consequence

C19orf38
NM_001136482.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

21 publications found

Variant links:

Genes affected

C19orf38 (HGNC:34073): (chromosome 19 open reading frame 38) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

C19orf38 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136482.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf38	NM_001136482.3	MANE Select	c.340+30G>A		intron	N/A	NP_001129954.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C19orf38	ENST00000397820.5	TSL:1 MANE Select	c.340+30G>A	intron	N/A	ENSP00000380920.3	A8MVS5
C19orf38	ENST00000592854.5	TSL:5	c.340+30G>A	intron	N/A	ENSP00000468568.1	A8MVS5
C19orf38	ENST00000872348.1		c.340+30G>A	intron	N/A	ENSP00000542407.1

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55294

AN:

151674

Hom.:

10202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.359

GnomAD2 exomes

AF:

0.377

AC:

57245

AN:

151706

AF XY:

0.381

show subpopulations

Gnomad AFR exome

AF:

0.328

Gnomad AMR exome

AF:

0.294

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.534

Gnomad FIN exome

AF:

0.408

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

AF:

0.385

AC:

537855

AN:

1395924

Hom.:

104755

Cov.:

AF XY:

0.385

AC XY:

265398

AN XY:

688654

show subpopulations

African (AFR)

AF:

0.326

AC:

10281

AN:

31570

American (AMR)

AF:

0.297

AC:

10598

AN:

35652

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

8777

AN:

25152

East Asian (EAS)

AF:

0.565

AC:

20194

AN:

35726

South Asian (SAS)

AF:

0.383

AC:

30316

AN:

79180

European-Finnish (FIN)

AF:

0.400

AC:

18979

AN:

47506

Middle Eastern (MID)

AF:

0.422

AC:

2401

AN:

5688

European-Non Finnish (NFE)

AF:

0.384

AC:

413932

AN:

1077496

Other (OTH)

AF:

0.386

AC:

22377

AN:

57954

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

18507

37015

55522

74030

92537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13242

26484

39726

52968

66210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.365

AC:

55373

AN:

151792

Hom.:

10235

Cov.:

AF XY:

0.367

AC XY:

27213

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.327

AC:

13539

AN:

41370

American (AMR)

AF:

0.320

AC:

4881

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1209

AN:

3458

East Asian (EAS)

AF:

0.568

AC:

2924

AN:

5144

South Asian (SAS)

AF:

0.373

AC:

1792

AN:

4802

European-Finnish (FIN)

AF:

0.409

AC:

4307

AN:

10538

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.375

AC:

25488

AN:

67912

Other (OTH)

AF:

0.359

AC:

757

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1795

3590

5385

7180

8975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.367

Hom.:

8271

Bravo

AF:

0.359

Asia WGS

AF:

0.439

AC:

1526

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.25

(source)

DANN

Benign

0.52

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over