rs963250

Variant names:

• chr4-115247002-A-G
• rs963250

Your query was ambiguous. Multiple possible variants found:

• chr4-115247002-A-G
• chr4-115247002-A-T

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 0.586 in 149,912 control chromosomes in the GnomAD database, including 29,078 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 0.59 (29078 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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: 0.586 AC: 87851 AN: 149790 Hom.: 29068 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.586 AC: 87880 AN: 149912 Hom.: 29078 Cov.: 30 AF XY: 0.588 AC XY: 42984 AN XY: 73150

African (AFR) AF: 0.339 AC: 13854 AN: 40924

American (AMR) AF: 0.656 AC: 9798 AN: 14936

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1812 AN: 3424

East Asian (EAS) AF: 0.639 AC: 3244 AN: 5078

South Asian (SAS) AF: 0.543 AC: 2563 AN: 4722

European-Finnish (FIN) AF: 0.724 AC: 7493 AN: 10354

Middle Eastern (MID) AF: 0.566 AC: 162 AN: 286

European-Non Finnish (NFE) AF: 0.698 AC: 46956 AN: 67228

Other (OTH) AF: 0.601 AC: 1233 AN: 2052

Alfa AF: 0.657 Hom.: 35452

Bravo AF: 0.578

Asia WGS AF: 0.561 AC: 1929 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.52
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs963250; hg19: chr4-116168158;