chr8-138500937-G-T

Variant names:

• chr8-138500937-G-T
• rs6577930

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 0.314 in 152,026 control chromosomes in the GnomAD database, including 11,590 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 0.31 (11590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 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 = 0.676 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: 0.314 AC: 47670 AN: 151908 Hom.: 11568 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.314 AC: 47744 AN: 152026 Hom.: 11590 Cov.: 32 AF XY: 0.309 AC XY: 22977 AN XY: 74300

African (AFR) AF: 0.682 AC: 28262 AN: 41418

American (AMR) AF: 0.214 AC: 3265 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3466

East Asian (EAS) AF: 0.186 AC: 961 AN: 5158

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11216 AN: 67998

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.265 Hom.: 1295

Bravo AF: 0.333

Asia WGS AF: 0.258 AC: 899 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	0.093
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6577930; hg19: chr8-139513180;