rs1470241

Variant names:

• chr13-88013628-T-C
• rs1470241

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 0.469 in 151,964 control chromosomes in the GnomAD database, including 19,031 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 (19031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.733 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: 0.469 AC: 71230 AN: 151846 Hom.: 19005 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.469 AC: 71293 AN: 151964 Hom.: 19031 Cov.: 32 AF XY: 0.467 AC XY: 34704 AN XY: 74284

African (AFR) AF: 0.740 AC: 30652 AN: 41446

American (AMR) AF: 0.365 AC: 5568 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1807 AN: 5154

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4820

European-Finnish (FIN) AF: 0.339 AC: 3572 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24142 AN: 67946

Other (OTH) AF: 0.457 AC: 964 AN: 2108

Alfa AF: 0.425 Hom.: 2038

Bravo AF: 0.480

Asia WGS AF: 0.431 AC: 1502 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1470241; hg19: chr13-88665883;