8-5368999-C-T

Variant names:

• chr8-5368999-C-T
• rs7003556

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 0.128 in 152,120 control chromosomes in the GnomAD database, including 1,407 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 0.13 (1407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.187 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: 0.128 AC: 19424 AN: 152002 Hom.: 1394 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.128 AC: 19484 AN: 152120 Hom.: 1407 Cov.: 32 AF XY: 0.127 AC XY: 9409 AN XY: 74362

African (AFR) AF: 0.190 AC: 7882 AN: 41464

American (AMR) AF: 0.0830 AC: 1269 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5184

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7644 AN: 67990

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.109 Hom.: 2059

Bravo AF: 0.127

Asia WGS AF: 0.0820 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.027
DANN	Benign	0.37
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7003556; hg19: chr8-5226521;