rs1340317

Variant names:

• chr13-64356863-T-A
• rs1340317

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 0.427 in 151,460 control chromosomes in the GnomAD database, including 14,245 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 0.43 (14245 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.511 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: 0.427 AC: 64577 AN: 151342 Hom.: 14222 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.427 AC: 64653 AN: 151460 Hom.: 14245 Cov.: 31 AF XY: 0.422 AC XY: 31191 AN XY: 73998

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.435

Alfa AF: 0.447 Hom.: 1929

Bravo AF: 0.444

Asia WGS AF: 0.356 AC: 1226 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0070
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340317; hg19: chr13-64930995;