chr8-19994623-G-A

Variant names:

• chr8-19994623-G-A
• rs17411024

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 0.118 in 152,062 control chromosomes in the GnomAD database, including 1,148 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 0.12 (1148 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).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.118 AC: 17902 AN: 151944 Hom.: 1149 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.118 AC: 17906 AN: 152062 Hom.: 1148 Cov.: 32 AF XY: 0.117 AC XY: 8694 AN XY: 74340

African (AFR) AF: 0.175 AC: 7235 AN: 41452

American (AMR) AF: 0.0849 AC: 1298 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.107 AC: 555 AN: 5170

South Asian (SAS) AF: 0.0958 AC: 461 AN: 4814

European-Finnish (FIN) AF: 0.0879 AC: 929 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6694 AN: 67984

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0537 Hom.: 62

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.89
DANN	Benign	0.20
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;