rs6932056

Variant names:

• chr6-137921300-T-C
• rs6932056

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0338 in 152,190 control chromosomes in the GnomAD database, including 98 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 0.034 (98 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0338 (5144/152190) while in subpopulation AFR AF = 0.0486 (2019/41530). AF 95% confidence interval is 0.0468. There are 98 homozygotes in GnomAd4. There are 2452 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 98 gene

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: 0.0338 AC: 5138 AN: 152072 Hom.: 98 Cov.: 33

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0338 AC: 5144 AN: 152190 Hom.: 98 Cov.: 33 AF XY: 0.0330 AC XY: 2452 AN XY: 74392

African (AFR) AF: 0.0486 AC: 2019 AN: 41530

American (AMR) AF: 0.0244 AC: 373 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3468

East Asian (EAS) AF: 0.0421 AC: 218 AN: 5172

South Asian (SAS) AF: 0.0424 AC: 204 AN: 4814

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1944 AN: 68006

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0325 Hom.: 223

Bravo AF: 0.0343

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.65
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs6932056; hg19: chr6-138242437;