rs1924298

Variant names:

• chr13-37609365-A-G
• rs1924298

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 0.202 in 152,024 control chromosomes in the GnomAD database, including 3,731 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 0.20 (3731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.202 AC: 30650 AN: 151906 Hom.: 3732 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.202 AC: 30653 AN: 152024 Hom.: 3731 Cov.: 32 AF XY: 0.201 AC XY: 14967 AN XY: 74314

Gnomad4 AFR AF: 0.0809

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.204

Alfa AF: 0.243 Hom.: 2381

Bravo AF: 0.184

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1924298; hg19: chr13-38183502;