8-55014157-G-T

Variant names:

• chr8-55014157-G-T
• rs10504176

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.146 in 152,178 control chromosomes in the GnomAD database, including 1,687 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 0.15 (1687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.146 AC: 22138 AN: 152060 Hom.: 1684 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.146 AC: 22168 AN: 152178 Hom.: 1687 Cov.: 32 AF XY: 0.143 AC XY: 10636 AN XY: 74402

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0625

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0772 Hom.: 104

Bravo AF: 0.147

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504176; hg19: chr8-55926717;