rs6929426

chr6-51432636-C-Achr6-51432636-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 0.347 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.368

Alfa AF: 0.347 Hom.: 1703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6929426; hg19: chr6-51297434;