rs13194053

Variant names:

• chr6-27176104-T-C
• rs13194053

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 0.14 in 152,204 control chromosomes in the GnomAD database, including 1,639 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 0.14 (1639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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 = 0.167 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: 0.140 AC: 21273 AN: 152088 Hom.: 1639 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.00845

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.140 AC: 21273 AN: 152204 Hom.: 1639 Cov.: 32 AF XY: 0.133 AC XY: 9913 AN XY: 74430

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.00847

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0903

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.126

Alfa AF: 0.157 Hom.: 3941

Bravo AF: 0.142

Asia WGS AF: 0.0590 AC: 205 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	2.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13194053; hg19: chr6-27143883;