chr8-19975135-G-T

Variant names:

• chr8-19975135-G-T
• rs17482753

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 0.0881 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
• Publications: 86 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0631 AC: 2623 AN: 41562

American (AMR) AF: 0.0798 AC: 1221 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3472

East Asian (EAS) AF: 0.108 AC: 557 AN: 5178

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4818

European-Finnish (FIN) AF: 0.0907 AC: 961 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6869 AN: 68016

Other (OTH) AF: 0.0872 AC: 184 AN: 2110

Alfa AF: 0.0962 Hom.: 3069

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17482753; hg19: chr8-19832646;