6-51432636-C-A

Variant names:

• chr6-51432636-C-A
• rs6929426

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 0.347 in 150,762 control chromosomes in the GnomAD database, including 9,586 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 (9586 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.494 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: 0.346 AC: 52189 AN: 150646 Hom.: 9568 Cov.: 28

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.347 AC: 52252 AN: 150762 Hom.: 9586 Cov.: 28 AF XY: 0.350 AC XY: 25736 AN XY: 73540

African (AFR) AF: 0.397 AC: 16268 AN: 40952

American (AMR) AF: 0.503 AC: 7623 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1260 AN: 5100

South Asian (SAS) AF: 0.319 AC: 1525 AN: 4788

European-Finnish (FIN) AF: 0.350 AC: 3589 AN: 10244

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19626 AN: 67762

Other (OTH) AF: 0.368 AC: 775 AN: 2104

Alfa AF: 0.366 Hom.: 4598

Bravo AF: 0.362

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs6929426; hg19: chr6-51297434;