chr13-61391170-T-G

Position:

• chr13-61391170-T-G

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 0.156 in 152,122 control chromosomes in the GnomAD database, including 2,097 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 0.16 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23636 AN: 152002 Hom.: 2088 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.156 AC: 23675 AN: 152122 Hom.: 2097 Cov.: 32 AF XY: 0.155 AC XY: 11493 AN XY: 74352

Gnomad4 AFR AF: 0.0770

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.160

Alfa AF: 0.186 Hom.: 1378

Bravo AF: 0.144

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.095
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2323266; hg19: chr13-61965303;