8-19994623-G-T

Position:

• chr8-19994623-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 42 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00670

Gnomad4 AMR AF: 0.0279

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0150

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0261

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.00327 Hom.: 55

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17411024; hg19: chr8-19852134;