rs1178061

chr6-50946658-C-T

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 0.43 in 151,880 control chromosomes in the GnomAD database, including 14,222 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 0.43 (14222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.430 AC: 65227 AN: 151760 Hom.: 14204 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.430 AC: 65279 AN: 151880 Hom.: 14222 Cov.: 32 AF XY: 0.424 AC XY: 31454 AN XY: 74222

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.401

Alfa AF: 0.438 Hom.: 1824

Bravo AF: 0.431

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.88
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1178061; hg19: chr6-50914371;