rs1340317

chr13-64356863-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;