8-127546912-C-T

Variant names:

• chr8-127546912-C-T
• rs6470531

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 0.395 in 151,976 control chromosomes in the GnomAD database, including 12,298 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 0.39 (12298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 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: 0.395 AC: 59933 AN: 151858 Hom.: 12273 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.395 AC: 59997 AN: 151976 Hom.: 12298 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74266

African (AFR) AF: 0.316 AC: 13101 AN: 41436

American (AMR) AF: 0.476 AC: 7266 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1736 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1425 AN: 5158

South Asian (SAS) AF: 0.357 AC: 1718 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5049 AN: 10536

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28339 AN: 67962

Other (OTH) AF: 0.414 AC: 876 AN: 2114

Alfa AF: 0.335 Hom.: 1447

Bravo AF: 0.390

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.36
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6470531; hg19: chr8-128559157;