rs13194053

Positions:

• chr6-27176104-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 0.14 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;