rs12753193

Variant names:

• chr1-65703996-G-A
• rs12753193
• ENST00000646875.2:n.37G>A

Variant summary

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

The ENST00000646875.2(ENSG00000285079):​n.37G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,242 control chromosomes in the GnomAD database, including 25,629 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 0.57 (25603 hom., cov: 32)
  • Exomes 𝑓: 0.57 (26 hom.)
• Consequence: ENSG00000285079 ENST00000646875.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 31 publications found

Genes affected

ENSG00000285079 (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 (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646875.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285079	ENST00000646875.2		n.37G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000285079	ENST00000760543.1		n.54G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000285079	ENST00000760544.1		n.-21G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86779 AN: 151958 Hom.: 25598 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.588

GnomAD4 exome AF: 0.572 AC: 95 AN: 166 Hom.: 26 Cov.: 0 AF XY: 0.592 AC XY: 58 AN XY: 98

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.250 AC: 4 AN: 16

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.545 AC: 12 AN: 22

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.603 AC: 70 AN: 116

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.571 AC: 86815 AN: 152076 Hom.: 25603 Cov.: 32 AF XY: 0.562 AC XY: 41753 AN XY: 74334

African (AFR) AF: 0.565 AC: 23413 AN: 41474

American (AMR) AF: 0.536 AC: 8191 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2169 AN: 3470

East Asian (EAS) AF: 0.125 AC: 644 AN: 5170

South Asian (SAS) AF: 0.539 AC: 2593 AN: 4810

European-Finnish (FIN) AF: 0.512 AC: 5417 AN: 10570

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42347 AN: 67972

Other (OTH) AF: 0.581 AC: 1226 AN: 2110

Alfa AF: 0.601 Hom.: 106153

Bravo AF: 0.573

Asia WGS AF: 0.367 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12753193; hg19: chr1-66169679;