rs1369976

Variant names:

• chr4-95886156-G-A
• rs1369976

Your query was ambiguous. Multiple possible variants found:

• chr4-95886156-G-A
• chr4-95886156-G-C

Variant summary

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

The variant allele was found at a frequency of 0.927 in 152,020 control chromosomes in the GnomAD database, including 65,333 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 0.93 (65333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140784 AN: 151902 Hom.: 65298 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.927 AC: 140874 AN: 152020 Hom.: 65333 Cov.: 32 AF XY: 0.928 AC XY: 68965 AN XY: 74302

African (AFR) AF: 0.925 AC: 38396 AN: 41504

American (AMR) AF: 0.934 AC: 14249 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3160 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5106 AN: 5116

South Asian (SAS) AF: 0.868 AC: 4187 AN: 4826

European-Finnish (FIN) AF: 0.971 AC: 10309 AN: 10618

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62387 AN: 67926

Other (OTH) AF: 0.925 AC: 1951 AN: 2110

Alfa AF: 0.908 Hom.: 83881

Bravo AF: 0.926

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.73
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1369976; hg19: chr4-96807307;