chr13-37609365-A-G

Variant names:

• chr13-37609365-A-G
• rs1924298
• ENST00000744989.1:n.48+12328A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000744989.1(ENSG00000297050):​n.48+12328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000297050 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000297050	ENST00000744989.1	n.48+12328A>G		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+12328A>G		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.0809 AC: 3357 AN: 41500

American (AMR) AF: 0.170 AC: 2590 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3470

East Asian (EAS) AF: 0.0633 AC: 328 AN: 5178

South Asian (SAS) AF: 0.136 AC: 656 AN: 4824

European-Finnish (FIN) AF: 0.335 AC: 3519 AN: 10514

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18700 AN: 67954

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.243 Hom.: 2632

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1924298; hg19: chr13-38183502;