chr4-115247081-C-G

Variant names:

• chr4-115247081-C-G
• rs963251

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 0.578 in 149,826 control chromosomes in the GnomAD database, including 28,475 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 0.58 (28475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.579 AC: 86627 AN: 149710 Hom.: 28464 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.556

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.578 AC: 86660 AN: 149826 Hom.: 28475 Cov.: 30 AF XY: 0.578 AC XY: 42292 AN XY: 73114

African (AFR) AF: 0.321 AC: 13088 AN: 40820

American (AMR) AF: 0.652 AC: 9765 AN: 14974

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1784 AN: 3422

East Asian (EAS) AF: 0.642 AC: 3249 AN: 5062

South Asian (SAS) AF: 0.535 AC: 2525 AN: 4716

European-Finnish (FIN) AF: 0.704 AC: 7281 AN: 10336

Middle Eastern (MID) AF: 0.563 AC: 161 AN: 286

European-Non Finnish (NFE) AF: 0.696 AC: 46829 AN: 67266

Other (OTH) AF: 0.596 AC: 1215 AN: 2040

Alfa AF: 0.599 Hom.: 3126

Bravo AF: 0.571

Asia WGS AF: 0.561 AC: 1932 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs963251; hg19: chr4-116168237;