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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807275.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304941	ENST00000807275.1		n.160+9397C>G		intron	N/A
	ENSG00000304941	ENST00000807276.1		n.208+9258C>G		intron	N/A
	ENSG00000304941	ENST00000807277.1		n.105+9397C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1764424;

hg19: chr13-96047182;