rs1319036

Variant names:

• chr8-69239817-C-T
• rs1319036

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 0.672 in 152,122 control chromosomes in the GnomAD database, including 35,531 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 0.67 (35531 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 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: 0.672 AC: 102149 AN: 152004 Hom.: 35522 Cov.: 33

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.672 AC: 102201 AN: 152122 Hom.: 35531 Cov.: 33 AF XY: 0.668 AC XY: 49693 AN XY: 74340

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.717

Alfa AF: 0.706 Hom.: 4802

Bravo AF: 0.670

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319036; hg19: chr8-70152052;