4-94421638-A-G

Variant names:

• chr4-94421638-A-G
• rs4699852

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.575 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

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.578

Alfa AF: 0.534 Hom.: 27122

Bravo AF: 0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4699852; hg19: chr4-95342789;