chr8-125465736-G-C

Variant names:

• chr8-125465736-G-C
• rs2001945

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 0.594 in 152,044 control chromosomes in the GnomAD database, including 27,980 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 0.59 (27980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 51 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90203 AN: 151926 Hom.: 27929 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.594 AC: 90307 AN: 152044 Hom.: 27980 Cov.: 32 AF XY: 0.589 AC XY: 43763 AN XY: 74302

African (AFR) AF: 0.790 AC: 32763 AN: 41472

American (AMR) AF: 0.501 AC: 7642 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2841 AN: 5176

South Asian (SAS) AF: 0.467 AC: 2246 AN: 4812

European-Finnish (FIN) AF: 0.552 AC: 5827 AN: 10558

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35585 AN: 67970

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.432 Hom.: 1152

Bravo AF: 0.598

Asia WGS AF: 0.551 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.72
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs2001945; hg19: chr8-126477978;