4-94435177-G-A

Variant names:

• chr4-94435177-G-A
• rs10008257

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 0.617 in 152,066 control chromosomes in the GnomAD database, including 30,341 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 0.62 (30341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.617 AC: 93769 AN: 151948 Hom.: 30283 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.617 AC: 93887 AN: 152066 Hom.: 30341 Cov.: 32 AF XY: 0.613 AC XY: 45550 AN XY: 74320

African (AFR) AF: 0.808 AC: 33547 AN: 41502

American (AMR) AF: 0.677 AC: 10348 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2167 AN: 5158

South Asian (SAS) AF: 0.379 AC: 1827 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5694 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36644 AN: 67946

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.569 Hom.: 64777

Bravo AF: 0.640

Asia WGS AF: 0.434 AC: 1508 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.35
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10008257; hg19: chr4-95356328;