rs6490970

Variant names:

• chr13-24660600-A-G
• rs6490970

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 0.466 in 152,036 control chromosomes in the GnomAD database, including 18,034 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 0.47 (18034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.467 AC: 70901 AN: 151918 Hom.: 18032 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.466 AC: 70918 AN: 152036 Hom.: 18034 Cov.: 32 AF XY: 0.468 AC XY: 34764 AN XY: 74294

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.518

Alfa AF: 0.551 Hom.: 21998

Bravo AF: 0.454

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6490970; hg19: chr13-25234738;