rs2251671

Variant names:

• chr8-40525297-T-C
• rs2251671

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 0.611 in 152,020 control chromosomes in the GnomAD database, including 29,034 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 (29034 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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: 0.611 AC: 92761 AN: 151902 Hom.: 29015 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.611 AC: 92819 AN: 152020 Hom.: 29034 Cov.: 31 AF XY: 0.614 AC XY: 45612 AN XY: 74314

African (AFR) AF: 0.467 AC: 19367 AN: 41442

American (AMR) AF: 0.648 AC: 9904 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3230 AN: 5154

South Asian (SAS) AF: 0.649 AC: 3120 AN: 4810

European-Finnish (FIN) AF: 0.729 AC: 7718 AN: 10582

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.663 AC: 45086 AN: 67970

Other (OTH) AF: 0.622 AC: 1316 AN: 2116

Alfa AF: 0.628 Hom.: 5306

Bravo AF: 0.600

Asia WGS AF: 0.604 AC: 2099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.46
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2251671; hg19: chr8-40382816;