rs1470241

chr13-88013628-T-C

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 0.469 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

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 (AFR) allele frequency at 95% confidence interval = 0.733 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: 0.469 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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.457

Alfa AF: 0.412 Hom.: 1823

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1470241; hg19: chr13-88665883;