dbSNP rs4097766: ENSG00000295014:n.604+1644C>T (chr1-157250762-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 ENST00000727371.1(ENSG00000295014):n.604+1644C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 152,116 control chromosomes in the GnomAD database, including 193 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 0.035 ( 193 hom., cov: 32)

Consequence

ENSG00000295014
ENST00000727371.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

0 publications found

Variant links:

Genes affected

ENSG00000295014 (HGNC:):

ENSG00000295014 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371456	XR_922183.3 link	n.510+1644C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000295014	ENST00000727371.1 link	n.604+1644C>T	intron_variant	Intron 2 of 3
ENSG00000295014	ENST00000727372.1 link	n.574+1644C>T	intron_variant	Intron 2 of 3
ENSG00000295014	ENST00000727373.1 link	n.510+1644C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0352

AC:

5356

AN:

152000

Hom.:

191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0402

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0987

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.0810

Gnomad SAS

AF:

0.0502

Gnomad FIN

AF:

0.0108

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0287

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

GnomAD4 genome

AF:

0.0353

AC:

5370

AN:

152116

Hom.:

193

Cov.:

AF XY:

0.0363

AC XY:

2703

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0403

AC:

1672

AN:

41504

American (AMR)

AF:

0.0990

AC:

1511

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.0810

AC:

419

AN:

5176

South Asian (SAS)

AF:

0.0499

AC:

240

AN:

4812

European-Finnish (FIN)

AF:

0.0108

AC:

114

AN:

10580

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0183

AC:

1241

AN:

67988

Other (OTH)

AF:

0.0299

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

254

509

763

1018

1272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.0121

Hom.:

Bravo

AF:

0.0429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.3

(source)

DANN

Benign

0.78

PhyloP100

-0.41

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