8-127501300-C-T

Variant names:

• chr8-127501300-C-T
• rs4871808

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 0.113 in 152,090 control chromosomes in the GnomAD database, including 1,228 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 0.11 (1228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• 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 (EAS) allele frequency at 95% confidence interval = 0.245 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: 0.113 AC: 17218 AN: 151972 Hom.: 1229 Cov.: 33

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.113 AC: 17214 AN: 152090 Hom.: 1228 Cov.: 33 AF XY: 0.114 AC XY: 8461 AN XY: 74328

African (AFR) AF: 0.0337 AC: 1401 AN: 41512

American (AMR) AF: 0.124 AC: 1896 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5176

South Asian (SAS) AF: 0.188 AC: 907 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10544

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9427 AN: 67982

Other (OTH) AF: 0.113 AC: 239 AN: 2116

Alfa AF: 0.129 Hom.: 4198

Bravo AF: 0.108

Asia WGS AF: 0.174 AC: 605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs4871808; hg19: chr8-128513545;