rs2319420

Variant names:

• chr8-139595064-C-T
• rs2319420

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 0.049 in 152,196 control chromosomes in the GnomAD database, including 696 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 0.049 (696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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: 0.0489 AC: 7441 AN: 152078 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0490 AC: 7452 AN: 152196 Hom.: 696 Cov.: 32 AF XY: 0.0554 AC XY: 4123 AN XY: 74404

African (AFR) AF: 0.0244 AC: 1012 AN: 41548

American (AMR) AF: 0.139 AC: 2116 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2085 AN: 5148

South Asian (SAS) AF: 0.0539 AC: 260 AN: 4822

European-Finnish (FIN) AF: 0.0690 AC: 732 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1108 AN: 68002

Other (OTH) AF: 0.0474 AC: 100 AN: 2110

Alfa AF: 0.0274 Hom.: 32

Bravo AF: 0.0551

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.60
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2319420; hg19: chr8-140607307; COSMIC: COSV69738832;