rs4694087

Positions:

• chr4-71053450-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;