8-130710456-T-A

Variant names:

• chr8-130710456-T-A
• rs1396977

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 0.42 in 151,938 control chromosomes in the GnomAD database, including 13,515 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 0.42 (13515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63732 AN: 151820 Hom.: 13494 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.420 AC: 63809 AN: 151938 Hom.: 13515 Cov.: 32 AF XY: 0.417 AC XY: 30968 AN XY: 74258

African (AFR) AF: 0.445 AC: 18446 AN: 41426

American (AMR) AF: 0.428 AC: 6545 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1016 AN: 3460

East Asian (EAS) AF: 0.480 AC: 2468 AN: 5140

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4810

European-Finnish (FIN) AF: 0.397 AC: 4196 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27502 AN: 67948

Other (OTH) AF: 0.386 AC: 815 AN: 2114

Alfa AF: 0.391 Hom.: 1448

Bravo AF: 0.422

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs1396977; hg19: chr8-131722702;