8-138500937-G-T

Position:

• chr8-138500937-G-T

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 0.314 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.270

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.093
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6577930; hg19: chr8-139513180;