rs1370051

chr13-57934694-G-Achr13-57934694-G-Cchr13-57934694-G-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 0.865 in 151,990 control chromosomes in the GnomAD database, including 59,655 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 0.86 (59655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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 = 0.991 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: 0.865 AC: 131360 AN: 151872 Hom.: 59635 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.865 AC: 131423 AN: 151990 Hom.: 59655 Cov.: 32 AF XY: 0.868 AC XY: 64434 AN XY: 74274

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.906

Alfa AF: 0.920 Hom.: 8249

Bravo AF: 0.848

Asia WGS AF: 0.885 AC: 3077 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	0.45
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370051; hg19: chr13-58508828;