rs11763972

Variant names:

• chr7-26614773-G-A
• rs11763972
• ENST00000661238.2:n.979+2475C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-26614773-G-A
• chr7-26614773-G-C

Variant summary

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

The ENST00000661238.2(ENSG00000286507):​n.979+2475C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,898 control chromosomes in the GnomAD database, including 2,024 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 0.16 (2024 hom., cov: 32)
• Consequence: ENSG00000286507 ENST00000661238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 6 publications found

Genes affected

ENSG00000286507 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661238.2. 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
	ENSG00000286507	ENST00000661238.2		n.979+2475C>T		intron	N/A
	ENSG00000286507	ENST00000719220.1		n.593+2475C>T		intron	N/A
	ENSG00000286507	ENST00000719221.1		n.481+2475C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23732 AN: 151780 Hom.: 2018 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.156 AC: 23751 AN: 151898 Hom.: 2024 Cov.: 32 AF XY: 0.157 AC XY: 11630 AN XY: 74244

African (AFR) AF: 0.157 AC: 6491 AN: 41398

American (AMR) AF: 0.201 AC: 3070 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.0368 AC: 190 AN: 5168

South Asian (SAS) AF: 0.161 AC: 775 AN: 4810

European-Finnish (FIN) AF: 0.192 AC: 2026 AN: 10538

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10376 AN: 67960

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.144 Hom.: 4712

Bravo AF: 0.156

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs11763972; hg19: chr7-26654392;