rs498670

Variant names:

• chr13-91111126-G-A
• rs498670

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 0.391 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.242 AC: 9966 AN: 41118

American (AMR) AF: 0.416 AC: 6324 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.106 AC: 545 AN: 5122

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4814

European-Finnish (FIN) AF: 0.366 AC: 3760 AN: 10276

Middle Eastern (MID) AF: 0.534 AC: 155 AN: 290

European-Non Finnish (NFE) AF: 0.504 AC: 34157 AN: 67782

Other (OTH) AF: 0.436 AC: 912 AN: 2094

Alfa AF: 0.469 Hom.: 36256

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs498670; hg19: chr13-91763380;