rs1013490

Positions:

• chr12-97070130-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000552238.1(ENSG00000258131):​n.39+84436T>C variant causes a intron, non coding transcript 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: ENST00000552238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000552238.1	n.39+84436T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000668647.1	n.297+36707T>C		intron_variant, non_coding_transcript_variant
	ENST00000666269.1	n.256-19576T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0465

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0410

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0530 Hom.: 58

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013490; hg19: chr12-97463908;