rs2532934

Positions:

• chr6-30926982-G-A

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 0.521 in 152,124 control chromosomes in the GnomAD database, including 21,727 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 0.52 (21727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79135 AN: 152006 Hom.: 21712 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.521 AC: 79185 AN: 152124 Hom.: 21727 Cov.: 33 AF XY: 0.533 AC XY: 39626 AN XY: 74384

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.522

Alfa AF: 0.547 Hom.: 41085

Bravo AF: 0.507

Asia WGS AF: 0.749 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.034
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2532934; hg19: chr6-30894759;