rs2001844

Variant names:

• chr8-125466503-A-G
• rs2001844

Your query was ambiguous. Multiple possible variants found:

• chr8-125466503-A-G
• chr8-125466503-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.380 AC: 15745 AN: 41472

American (AMR) AF: 0.365 AC: 5587 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2761 AN: 5172

South Asian (SAS) AF: 0.347 AC: 1671 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4948 AN: 10568

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32070 AN: 67982

Other (OTH) AF: 0.427 AC: 903 AN: 2114

Alfa AF: 0.416 Hom.: 3302

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

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