dbSNP rs17439810: ENSG00000293349:n.810C>G (chr4-40043720-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000381811.2(ENSG00000293349):n.810C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,599,574 control chromosomes in the GnomAD database, including 50,963 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 0.21 ( 3773 hom., cov: 31)

Exomes 𝑓: 0.25 ( 47190 hom. )

Consequence

ENSG00000293349
ENST00000381811.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0530

Publications

9 publications found

Variant links:

Genes affected

ENSG00000293349 (HGNC:):

ENSG00000293349 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC344967	NR_027277.2 link	n.810C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293349	ENST00000381811.2 link	n.810C>G		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000205794	ENST00000507914.2 link	n.416C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31829

AN:

151914

Hom.:

3779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.0569

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.264

GnomAD2 exomes

AF:

0.215

AC:

54043

AN:

250842

AF XY:

0.222

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.156

Gnomad ASJ exome

AF:

0.327

Gnomad EAS exome

AF:

0.0607

Gnomad FIN exome

AF:

0.234

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.242

GnomAD4 exome

AF:

0.249

AC:

360562

AN:

1447542

Hom.:

47190

Cov.:

AF XY:

0.249

AC XY:

179091

AN XY:

720542

show subpopulations

African (AFR)

AF:

0.112

AC:

3736

AN:

33226

American (AMR)

AF:

0.161

AC:

7153

AN:

44478

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

8415

AN:

25962

East Asian (EAS)

AF:

0.0604

AC:

2388

AN:

39542

South Asian (SAS)

AF:

0.185

AC:

15902

AN:

86026

European-Finnish (FIN)

AF:

0.232

AC:

12286

AN:

52986

Middle Eastern (MID)

AF:

0.304

AC:

1745

AN:

5740

European-Non Finnish (NFE)

AF:

0.267

AC:

293850

AN:

1099832

Other (OTH)

AF:

0.253

AC:

15087

AN:

59750

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

15209

30419

45628

60838

76047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9720

19440

29160

38880

48600

<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:

0.209

AC:

31816

AN:

152032

Hom.:

3773

Cov.:

AF XY:

0.206

AC XY:

15303

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.117

AC:

4853

AN:

41468

American (AMR)

AF:

0.222

AC:

3384

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

1150

AN:

3472

East Asian (EAS)

AF:

0.0570

AC:

295

AN:

5176

South Asian (SAS)

AF:

0.166

AC:

800

AN:

4820

European-Finnish (FIN)

AF:

0.233

AC:

2462

AN:

10568

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.266

AC:

18089

AN:

67964

Other (OTH)

AF:

0.263

AC:

554

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1263

2527

3790

5054

6317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.248

Hom.:

930

Bravo

AF:

0.206

Asia WGS

AF:

0.125

AC:

436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

0.053

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over