12-110451052-C-T

Variant names:

• chr12-110451052-C-T
• rs3759384
• ENST00000772605.1:n.955C>T

Variant summary

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

The ENST00000772605.1(ENSG00000300534):​n.955C>T 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 0.477 in 151,576 control chromosomes in the GnomAD database, including 19,774 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 0.48 (19774 hom., cov: 30)
• Consequence: ENSG00000300534 ENST00000772605.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 13 publications found

Genes affected

ENSG00000300534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772605.1. 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
	ENSG00000300534	ENST00000772605.1		n.955C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000300534	ENST00000772597.1		n.66+712C>T		intron	N/A
	ENSG00000300534	ENST00000772598.1		n.496+712C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72139 AN: 151458 Hom.: 19727 Cov.: 30

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.477 AC: 72250 AN: 151576 Hom.: 19774 Cov.: 30 AF XY: 0.472 AC XY: 34914 AN XY: 74036

African (AFR) AF: 0.755 AC: 31199 AN: 41326

American (AMR) AF: 0.456 AC: 6925 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3466

East Asian (EAS) AF: 0.0898 AC: 464 AN: 5166

South Asian (SAS) AF: 0.272 AC: 1306 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4421 AN: 10444

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25464 AN: 67886

Other (OTH) AF: 0.449 AC: 940 AN: 2094

Alfa AF: 0.423 Hom.: 1774

Bravo AF: 0.492

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16

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: rs3759384; hg19: chr12-110888857;