6-50885174-C-A

Variant names:

• chr6-50885174-C-A
• rs2143881

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 0.354 in 151,952 control chromosomes in the GnomAD database, including 10,884 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 0.35 (10884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53787 AN: 151834 Hom.: 10887 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.354 AC: 53798 AN: 151952 Hom.: 10884 Cov.: 32 AF XY: 0.351 AC XY: 26087 AN XY: 74258

African (AFR) AF: 0.152 AC: 6312 AN: 41486

American (AMR) AF: 0.350 AC: 5337 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2494 AN: 5164

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4046 AN: 10538

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31222 AN: 67922

Other (OTH) AF: 0.356 AC: 751 AN: 2112

Alfa AF: 0.394 Hom.: 1592

Bravo AF: 0.343

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.21
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2143881; hg19: chr6-50852887;