8-46503462-C-T

Variant names:

• chr8-46503462-C-T
• rs4313171

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 0.164 in 150,184 control chromosomes in the GnomAD database, including 4,079 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 0.16 (4079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.164 AC: 24539 AN: 150066 Hom.: 4066 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0944

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.164 AC: 24597 AN: 150184 Hom.: 4079 Cov.: 32 AF XY: 0.164 AC XY: 12061 AN XY: 73378

African (AFR) AF: 0.408 AC: 16799 AN: 41136

American (AMR) AF: 0.186 AC: 2789 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.0944 AC: 324 AN: 3432

East Asian (EAS) AF: 0.134 AC: 683 AN: 5094

South Asian (SAS) AF: 0.178 AC: 856 AN: 4810

European-Finnish (FIN) AF: 0.0400 AC: 424 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0354 AC: 2366 AN: 66816

Other (OTH) AF: 0.152 AC: 316 AN: 2078

Alfa AF: 0.0328 Hom.: 69

Bravo AF: 0.187

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Other links and lift over

dbSNP: rs4313171; hg19: chr8-47415084;