rs6492538

Variant names:

• chr13-91341492-A-C
• rs6492538

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 0.824 in 152,146 control chromosomes in the GnomAD database, including 52,458 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 0.82 (52458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 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: 0.824 AC: 125267 AN: 152028 Hom.: 52396 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.824 AC: 125390 AN: 152146 Hom.: 52458 Cov.: 32 AF XY: 0.818 AC XY: 60852 AN XY: 74358

African (AFR) AF: 0.960 AC: 39879 AN: 41556

American (AMR) AF: 0.786 AC: 12016 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2874 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4265 AN: 5178

South Asian (SAS) AF: 0.876 AC: 4220 AN: 4820

European-Finnish (FIN) AF: 0.643 AC: 6801 AN: 10580

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52482 AN: 67944

Other (OTH) AF: 0.841 AC: 1777 AN: 2114

Alfa AF: 0.794 Hom.: 6034

Bravo AF: 0.838

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.70
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6492538; hg19: chr13-91993746;