13-61357366-A-T

Variant names:

• chr13-61357366-A-T
• rs10507665

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 0.0355 in 152,330 control chromosomes in the GnomAD database, including 124 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 0.036 (124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 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: 0.0355 AC: 5402 AN: 152212 Hom.: 124 Cov.: 32

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0355 AC: 5408 AN: 152330 Hom.: 124 Cov.: 32 AF XY: 0.0355 AC XY: 2643 AN XY: 74480

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.00345 Hom.: 0

Bravo AF: 0.0389

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507665; hg19: chr13-61931499;