12-105934476-T-C

Variant names:

• chr12-105934476-T-C
• rs2111980
• ENST00000812786.1:n.39T>C

Variant summary

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

The ENST00000812786.1(ENSG00000305754):​n.39T>C 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 0.485 in 151,970 control chromosomes in the GnomAD database, including 18,670 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 (18670 hom., cov: 31)
• Consequence: ENSG00000305754 ENST00000812786.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 16 publications found

Genes affected

ENSG00000305754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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
ENSG00000305754	ENST00000812786.1	n.39T>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000305754	ENST00000812783.1	n.-14T>C		upstream_gene_variant
ENSG00000305754	ENST00000812784.1	n.-105T>C		upstream_gene_variant
ENSG00000305754	ENST00000812785.1	n.-161T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73671 AN: 151852 Hom.: 18670 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.485 AC: 73681 AN: 151970 Hom.: 18670 Cov.: 31 AF XY: 0.488 AC XY: 36211 AN XY: 74264

African (AFR) AF: 0.325 AC: 13456 AN: 41434

American (AMR) AF: 0.488 AC: 7460 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2087 AN: 5166

South Asian (SAS) AF: 0.535 AC: 2564 AN: 4796

European-Finnish (FIN) AF: 0.620 AC: 6539 AN: 10554

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38235 AN: 67958

Other (OTH) AF: 0.461 AC: 972 AN: 2110

Alfa AF: 0.525 Hom.: 67425

Bravo AF: 0.466

Asia WGS AF: 0.445 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs2111980; hg19: chr12-106328254;