Genetic Variant ENST00000435946.1:n.139-89799G>T (chr6-74257276-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435946.1(ENSG00000223786):n.139-89799G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,002 control chromosomes in the GnomAD database, including 10,656 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 0.34 ( 10656 hom., cov: 32)

Consequence

ENSG00000223786
ENST00000435946.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

3 publications found

Variant links:

Genes affected

ENSG00000223786 (HGNC:):

ENSG00000223786 links:

Genome browser will be placed here

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=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928516	NR_110856.1 link	n.139-89799G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223786	ENST00000435946.1 link	n.139-89799G>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51600

AN:

151884

Hom.:

10658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0923

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.444

Gnomad OTH

AF:

0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.339

AC:

51603

AN:

152002

Hom.:

10656

Cov.:

AF XY:

0.342

AC XY:

25433

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.0922

AC:

3825

AN:

41502

American (AMR)

AF:

0.408

AC:

6235

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1182

AN:

3466

East Asian (EAS)

AF:

0.439

AC:

2263

AN:

5160

South Asian (SAS)

AF:

0.501

AC:

2411

AN:

4816

European-Finnish (FIN)

AF:

0.409

AC:

4304

AN:

10530

Middle Eastern (MID)

AF:

0.394

AC:

115

AN:

292

European-Non Finnish (NFE)

AF:

0.444

AC:

30187

AN:

67944

Other (OTH)

AF:

0.352

AC:

743

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1563

3126

4689

6252

7815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.382

Hom.:

2119

Bravo

AF:

0.325

Asia WGS

AF:

0.459

AC:

1598

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.64

PhyloP100

1.3

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over