rs1757948

Variant names:

• chr9-78695764-A-C
• rs1757948
• ENST00000761518.1:n.140+497A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-78695764-A-C
• chr9-78695764-A-G
• chr9-78695764-A-T

Variant summary

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

The ENST00000761518.1(ENSG00000299197):​n.140+497A>C variant causes a intron change. The variant allele was found at a frequency of 0.262 in 151,818 control chromosomes in the GnomAD database, including 6,293 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 0.26 (6293 hom., cov: 32)
• Consequence: ENSG00000299197 ENST00000761518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.65
• Publications: 11 publications found

Genes affected

ENSG00000299197 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761518.1. 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
	ENSG00000299197	ENST00000761518.1		n.140+497A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39757 AN: 151698 Hom.: 6285 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 151818 Hom.: 6293 Cov.: 32 AF XY: 0.267 AC XY: 19831 AN XY: 74170

African (AFR) AF: 0.0844 AC: 3503 AN: 41482

American (AMR) AF: 0.368 AC: 5619 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2072 AN: 5130

South Asian (SAS) AF: 0.193 AC: 930 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4034 AN: 10504

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21596 AN: 67856

Other (OTH) AF: 0.289 AC: 608 AN: 2106

Alfa AF: 0.290 Hom.: 16598

Bravo AF: 0.258

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.55
PhyloP100		5.7

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: rs1757948;

hg19: chr9-81310680;

COSMIC: COSV60363461;