rs12585734

Variant names:

• chr13-76293531-G-A
• rs12585734
• ENST00000753498.1:n.208+25921G>A

Variant summary

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

The ENST00000753498.1(ENSG00000298166):​n.208+25921G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,022 control chromosomes in the GnomAD database, including 382 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 0.054 (382 hom., cov: 32)
• Consequence: ENSG00000298166 ENST00000753498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 0 publications found

Genes affected

ENSG00000298166 (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 (EAS) allele frequency at 95% confidence interval = 0.231 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
ENSG00000298166	ENST00000753498.1	n.208+25921G>A		intron_variant	Intron 2 of 2
ENSG00000298166	ENST00000753499.1	n.118+25921G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8190 AN: 151904 Hom.: 377 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0505

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

GnomAD4 genome AF: 0.0540 AC: 8208 AN: 152022 Hom.: 382 Cov.: 32 AF XY: 0.0562 AC XY: 4172 AN XY: 74300

African (AFR) AF: 0.0124 AC: 513 AN: 41520

American (AMR) AF: 0.0658 AC: 1004 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1248 AN: 5158

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4820

European-Finnish (FIN) AF: 0.0808 AC: 854 AN: 10564

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0564 AC: 3830 AN: 67926

Other (OTH) AF: 0.0571 AC: 120 AN: 2102

Alfa AF: 0.0574 Hom.: 482

Bravo AF: 0.0549

Asia WGS AF: 0.161 AC: 557 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.44
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12585734; hg19: chr13-76867667; COSMIC: COSV69365756;