rs1178061

Variant names:

• chr6-50946658-C-T
• rs1178061

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.412 AC: 17039 AN: 41398

American (AMR) AF: 0.380 AC: 5794 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1424 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2470 AN: 5132

South Asian (SAS) AF: 0.352 AC: 1695 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4052 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31323 AN: 67956

Other (OTH) AF: 0.401 AC: 847 AN: 2110

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1178061; hg19: chr6-50914371;