rs2319420

Positions:

• chr8-139595064-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.0539

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0273 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

Splicing

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

Publications

LitVar

Other links and lift over

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