rs1764424

Variant names:

• chr13-95394928-G-C
• rs1764424
• ENST00000807275.1:n.160+9397C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-95394928-G-C
• chr13-95394928-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807275.1(ENSG00000304941):​n.160+9397C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,632 control chromosomes in the GnomAD database, including 13,749 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 0.39 (13749 hom., cov: 28)
• Consequence: ENSG00000304941 ENST00000807275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 1 publications found

Genes affected

ENSG00000304941 (HGNC:):

ACMG classification

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 = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903193	XR_007063839.1	n.764+9397C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304941	ENST00000807275.1	n.160+9397C>G		intron_variant	Intron 1 of 1
ENSG00000304941	ENST00000807276.1	n.208+9258C>G		intron_variant	Intron 1 of 1
ENSG00000304941	ENST00000807277.1	n.105+9397C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59528 AN: 151514 Hom.: 13751 Cov.: 28

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.393 AC: 59548 AN: 151632 Hom.: 13749 Cov.: 28 AF XY: 0.393 AC XY: 29093 AN XY: 74034

African (AFR) AF: 0.134 AC: 5525 AN: 41382

American (AMR) AF: 0.435 AC: 6586 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1450 AN: 3462

East Asian (EAS) AF: 0.545 AC: 2805 AN: 5146

South Asian (SAS) AF: 0.357 AC: 1713 AN: 4804

European-Finnish (FIN) AF: 0.502 AC: 5257 AN: 10478

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34812 AN: 67912

Other (OTH) AF: 0.411 AC: 860 AN: 2092

Alfa AF: 0.439 Hom.: 1943

Bravo AF: 0.382

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.44
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1764424; hg19: chr13-96047182;