rs4694087

Variant names:

• chr4-71053450-G-C
• rs4694087

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 0.609 in 151,966 control chromosomes in the GnomAD database, including 30,786 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 0.61 (30786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.609 AC: 92505 AN: 151848 Hom.: 30785 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.609 AC: 92521 AN: 151966 Hom.: 30786 Cov.: 32 AF XY: 0.610 AC XY: 45305 AN XY: 74282

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.671

Alfa AF: 0.649 Hom.: 4188

Bravo AF: 0.606

Asia WGS AF: 0.717 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
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: rs4694087; hg19: chr4-71919167;