rs498670

chr13-91111126-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 0.391 in 151,062 control chromosomes in the GnomAD database, including 12,837 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 (12837 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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: 59082 AN: 150944 Hom.: 12839 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.391 AC: 59086 AN: 151062 Hom.: 12837 Cov.: 30 AF XY: 0.380 AC XY: 28002 AN XY: 73784

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.436

Alfa AF: 0.478 Hom.: 23718

Bravo AF: 0.392

Asia WGS AF: 0.168 AC: 584 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.61
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs498670; hg19: chr13-91763380;