4-94421638-A-G

Variant names:

• chr4-94421638-A-G
• rs4699852

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 0.575 in 151,584 control chromosomes in the GnomAD database, including 25,470 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 (25470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• 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 (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87090 AN: 151462 Hom.: 25431 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.575 AC: 87183 AN: 151584 Hom.: 25470 Cov.: 31 AF XY: 0.572 AC XY: 42372 AN XY: 74014

African (AFR) AF: 0.668 AC: 27660 AN: 41386

American (AMR) AF: 0.651 AC: 9897 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1725 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2349 AN: 5146

South Asian (SAS) AF: 0.378 AC: 1824 AN: 4820

European-Finnish (FIN) AF: 0.536 AC: 5605 AN: 10458

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36295 AN: 67802

Other (OTH) AF: 0.578 AC: 1219 AN: 2108

Alfa AF: 0.542 Hom.: 36102

Bravo AF: 0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.35
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4699852; hg19: chr4-95342789;