13-37561466-G-C

Position:

• chr13-37561466-G-C

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 0.708 in 152,106 control chromosomes in the GnomAD database, including 38,508 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 0.71 (38508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.708 AC: 107549 AN: 151990 Hom.: 38472 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.708 AC: 107633 AN: 152106 Hom.: 38508 Cov.: 32 AF XY: 0.716 AC XY: 53268 AN XY: 74368

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.690

Alfa AF: 0.678 Hom.: 4381

Bravo AF: 0.707

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.067
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7994218; hg19: chr13-38135603;