rs12525670

Variant names:

• chr6-159604439-C-T
• rs12525670
• ENST00000656085.1:n.42+58147G>A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+58147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,118 control chromosomes in the GnomAD database, including 5,169 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 (5169 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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
ENSG00000286533	ENST00000656085.1	n.42+58147G>A		intron_variant	Intron 1 of 1
ENSG00000286533	ENST00000794978.1	n.186-9235G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36014 AN: 152000 Hom.: 5164 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.237 AC: 36047 AN: 152118 Hom.: 5169 Cov.: 32 AF XY: 0.235 AC XY: 17512 AN XY: 74372

African (AFR) AF: 0.412 AC: 17104 AN: 41468

American (AMR) AF: 0.180 AC: 2752 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.179 AC: 924 AN: 5164

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4814

European-Finnish (FIN) AF: 0.164 AC: 1735 AN: 10596

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11170 AN: 67996

Other (OTH) AF: 0.215 AC: 455 AN: 2116

Alfa AF: 0.190 Hom.: 4168

Bravo AF: 0.245

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12525670; hg19: chr6-160025471;