chr12-53209954-A-G

Variant names:

• chr12-53209954-A-G
• rs1554753
• ENST00000748275.1:n.112A>G

Variant summary

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

The ENST00000748275.1(ENSG00000297487):​n.112A>G 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 0.327 in 152,088 control chromosomes in the GnomAD database, including 9,568 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 0.33 (9568 hom., cov: 32)
• Consequence: ENSG00000297487 ENST00000748275.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 12 publications found

Genes affected

ENSG00000297487 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748275.1. 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
	ENSG00000297487	ENST00000748275.1		n.112A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49572 AN: 151968 Hom.: 9527 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.327 AC: 49669 AN: 152088 Hom.: 9568 Cov.: 32 AF XY: 0.337 AC XY: 25025 AN XY: 74344

African (AFR) AF: 0.510 AC: 21122 AN: 41442

American (AMR) AF: 0.322 AC: 4914 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2538 AN: 5164

South Asian (SAS) AF: 0.491 AC: 2371 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13573 AN: 68008

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.233 Hom.: 9641

Bravo AF: 0.328

Asia WGS AF: 0.516 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.71
PhyloP100		0.028

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1554753;

hg19: chr12-53603738;