rs6492538

Positions:

• chr13-91341492-A-C

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 0.824 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.841

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6492538; hg19: chr13-91993746;