8-19994623-G-T

Variant names:

• chr8-19994623-G-T
• rs17411024

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0189 in 152,108 control chromosomes in the GnomAD database, including 42 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 0.019 (42 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0189 (2868/152108) while in subpopulation AMR AF = 0.0279 (427/15290). AF 95% confidence interval is 0.0257. There are 42 homozygotes in GnomAd4. There are 1374 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 42 gene

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: 0.0189 AC: 2871 AN: 151990 Hom.: 42 Cov.: 32

Gnomad AFR AF: 0.00672

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0254

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

GnomAD4 genome AF: 0.0189 AC: 2868 AN: 152108 Hom.: 42 Cov.: 32 AF XY: 0.0185 AC XY: 1374 AN XY: 74364

African (AFR) AF: 0.00670 AC: 278 AN: 41474

American (AMR) AF: 0.0279 AC: 427 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0150 AC: 72 AN: 4816

European-Finnish (FIN) AF: 0.0179 AC: 189 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1776 AN: 67994

Other (OTH) AF: 0.0246 AC: 52 AN: 2112

Alfa AF: 0.00315 Hom.: 62

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.72
DANN	Benign	0.31
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17411024; hg19: chr8-19852134;