rs532098

Variant names:

• chr6-32610275-G-A
• rs532098

Your query was ambiguous. Multiple possible variants found:

• chr6-32610275-G-A
• chr6-32610275-G-C
• chr6-32610275-G-T

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 0.432 in 152,062 control chromosomes in the GnomAD database, including 14,437 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 0.43 (14437 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 69 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 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: 0.432 AC: 65707 AN: 151944 Hom.: 14429 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.432 AC: 65749 AN: 152062 Hom.: 14437 Cov.: 31 AF XY: 0.432 AC XY: 32148 AN XY: 74354

African (AFR) AF: 0.388 AC: 16077 AN: 41444

American (AMR) AF: 0.509 AC: 7786 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2190 AN: 5176

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4818

European-Finnish (FIN) AF: 0.434 AC: 4594 AN: 10586

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30117 AN: 67972

Other (OTH) AF: 0.438 AC: 923 AN: 2106

Alfa AF: 0.440 Hom.: 32486

Bravo AF: 0.442

Asia WGS AF: 0.392 AC: 1362 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	4.8
DANN	Benign	0.84
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs532098; hg19: chr6-32578052;