rs1013490

Variant names:

• chr12-97070130-T-C
• rs1013490
• ENST00000666269.1:n.256-19576T>C

Variant summary

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

The ENST00000666269.1(ENSG00000257470):​n.256-19576T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,198 control chromosomes in the GnomAD database, including 595 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 0.077 (595 hom., cov: 33)
• Consequence: ENSG00000257470 ENST00000666269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 2 publications found

Genes affected

ENSG00000257470 (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 (AMR) allele frequency at 95% confidence interval = 0.152 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
ENSG00000257470	ENST00000666269.1	n.256-19576T>C		intron_variant	Intron 3 of 3
ENSG00000257470	ENST00000668647.1	n.297+36707T>C		intron_variant	Intron 3 of 3
ENSG00000257470	ENST00000716365.1	n.205+36707T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11658 AN: 152080 Hom.: 591 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0465

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0767 AC: 11676 AN: 152198 Hom.: 595 Cov.: 33 AF XY: 0.0809 AC XY: 6023 AN XY: 74420

African (AFR) AF: 0.101 AC: 4193 AN: 41544

American (AMR) AF: 0.157 AC: 2398 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0465 AC: 161 AN: 3466

East Asian (EAS) AF: 0.116 AC: 602 AN: 5188

South Asian (SAS) AF: 0.119 AC: 576 AN: 4822

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0410 AC: 2790 AN: 67968

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.0543 Hom.: 64

Bravo AF: 0.0836

Asia WGS AF: 0.114 AC: 401 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	5.3
DANN	Benign	0.58
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1013490; hg19: chr12-97463908;