rs6490970

Variant names:

• chr13-24660600-A-G
• rs6490970

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 0.466 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.264 AC: 10959 AN: 41458

American (AMR) AF: 0.546 AC: 8342 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2103 AN: 3466

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5174

South Asian (SAS) AF: 0.444 AC: 2134 AN: 4806

European-Finnish (FIN) AF: 0.604 AC: 6379 AN: 10556

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38076 AN: 67982

Other (OTH) AF: 0.518 AC: 1094 AN: 2110

Alfa AF: 0.530 Hom.: 54508

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs6490970; hg19: chr13-25234738;