rs4557669

chr8-126294357-C-T

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 0.747 in 151,984 control chromosomes in the GnomAD database, including 42,607 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 0.75 (42607 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113511 AN: 151866 Hom.: 42561 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.748 AC: 113608 AN: 151984 Hom.: 42607 Cov.: 31 AF XY: 0.744 AC XY: 55256 AN XY: 74232

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.743

Alfa AF: 0.741 Hom.: 70791

Bravo AF: 0.746

Asia WGS AF: 0.687 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.27
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4557669; hg19: chr8-127306602;