8-19975135-G-T

Variant names:

• chr8-19975135-G-T
• rs17482753

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 0.0881 in 152,260 control chromosomes in the GnomAD database, including 590 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 0.088 (590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 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: 0.0882 AC: 13425 AN: 152142 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0907

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0881 AC: 13414 AN: 152260 Hom.: 590 Cov.: 32 AF XY: 0.0875 AC XY: 6516 AN XY: 74446

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.0907

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0988 Hom.: 1478

Bravo AF: 0.0855

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17482753; hg19: chr8-19832646;