rs2001844

chr8-125466503-A-Gchr8-125466503-A-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 0.432 in 152,098 control chromosomes in the GnomAD database, including 14,350 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 0.43 (14350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.432 AC: 65598 AN: 151980 Hom.: 14324 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.432 AC: 65661 AN: 152098 Hom.: 14350 Cov.: 32 AF XY: 0.427 AC XY: 31720 AN XY: 74364

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.427

Alfa AF: 0.445 Hom.: 2227

Bravo AF: 0.426

Asia WGS AF: 0.462 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	12
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001844; hg19: chr8-126478745; COSMIC: COSV72956545;