12-27812217-C-T

Variant names:

• chr12-27812217-C-T
• rs10842994
• ENST00000825469.1:n.320+1127C>T

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.320+1127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,278 control chromosomes in the GnomAD database, including 2,090 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 0.15 (2090 hom., cov: 33)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 101 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369709	XR_931459.3	n.246-816G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257042	ENST00000825469.1	n.320+1127C>T		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.175+1127C>T		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.140+1127C>T		intron_variant	Intron 1 of 1
ENSG00000307385	ENST00000825567.1	n.254-816G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22787 AN: 152160 Hom.: 2091 Cov.: 33

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.150 AC: 22792 AN: 152278 Hom.: 2090 Cov.: 33 AF XY: 0.148 AC XY: 10990 AN XY: 74448

African (AFR) AF: 0.0445 AC: 1849 AN: 41574

American (AMR) AF: 0.167 AC: 2559 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1031 AN: 5178

South Asian (SAS) AF: 0.143 AC: 692 AN: 4828

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13713 AN: 68010

Other (OTH) AF: 0.152 AC: 322 AN: 2114

Alfa AF: 0.178 Hom.: 7393

Bravo AF: 0.143

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.5
DANN	Benign	0.77
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs10842994; hg19: chr12-27965150;