rs5000634

chr6-32695787-A-G

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 0.391 in 150,540 control chromosomes in the GnomAD database, including 11,851 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 0.39 (11851 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.391 AC: 58866 AN: 150422 Hom.: 11839 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.391 AC: 58920 AN: 150540 Hom.: 11851 Cov.: 31 AF XY: 0.393 AC XY: 28841 AN XY: 73456

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.411

Alfa AF: 0.393 Hom.: 14943

Bravo AF: 0.403

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.9
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5000634; hg19: chr6-32663564;