13-108166537-T-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 0.0975 in 152,200 control chromosomes in the GnomAD database, including 900 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 0.098 (900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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 = 0.172 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: 0.0977 AC: 14852 AN: 152082 Hom.: 902 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0975 AC: 14845 AN: 152200 Hom.: 900 Cov.: 32 AF XY: 0.0956 AC XY: 7114 AN XY: 74422

Gnomad4 AFR AF: 0.0451

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0901

Alfa AF: 0.113 Hom.: 1556

Bravo AF: 0.0986

Asia WGS AF: 0.147 AC: 511 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	3.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8002852; hg19: chr13-108818885;