rs258415

Variant names:

• chr12-27864589-A-C
• rs258415
• ENST00000825469.1:n.320+53499A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-27864589-A-C
• chr12-27864589-A-G
• chr12-27864589-A-T

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.320+53499A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,134 control chromosomes in the GnomAD database, including 5,227 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 0.24 (5227 hom., cov: 32)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 25 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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
ENSG00000257042	ENST00000825469.1	n.320+53499A>C		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.175+53499A>C		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.140+53499A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36385 AN: 152016 Hom.: 5216 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.239 AC: 36429 AN: 152134 Hom.: 5227 Cov.: 32 AF XY: 0.235 AC XY: 17491 AN XY: 74370

African (AFR) AF: 0.402 AC: 16662 AN: 41492

American (AMR) AF: 0.167 AC: 2553 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1391 AN: 5168

South Asian (SAS) AF: 0.151 AC: 727 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1433 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12354 AN: 67978

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.199 Hom.: 5749

Bravo AF: 0.249

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.38
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs258415; hg19: chr12-28017522;