8-6971563-G-T

Variant names:

• chr8-6971563-G-T
• rs2738113

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 0.584 in 151,926 control chromosomes in the GnomAD database, including 26,090 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 0.58 (26090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.761
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88626 AN: 151808 Hom.: 26044 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.584 AC: 88732 AN: 151926 Hom.: 26090 Cov.: 32 AF XY: 0.585 AC XY: 43441 AN XY: 74246

African (AFR) AF: 0.629 AC: 26013 AN: 41374

American (AMR) AF: 0.567 AC: 8660 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2772 AN: 5152

South Asian (SAS) AF: 0.600 AC: 2886 AN: 4812

European-Finnish (FIN) AF: 0.564 AC: 5966 AN: 10578

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38849 AN: 67960

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.567 Hom.: 49359

Bravo AF: 0.582

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.34
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2738113; hg19: chr8-6829085;