8-125465736-G-C

Variant names:

• chr8-125465736-G-C
• rs2001945

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 0.594 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.594 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

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.565

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001945; hg19: chr8-126477978;