12-127239387-C-T

Variant names:

• chr12-127239387-C-T
• rs3851660
• ENST00000755538.1:n.391-14077C>T

Variant summary

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

The ENST00000755538.1(ENSG00000286791):​n.391-14077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,282 control chromosomes in the GnomAD database, including 70 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 0.027 (70 hom., cov: 33)
• Consequence: ENSG00000286791 ENST00000755538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 publications found

Genes affected

ENSG00000286791 (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 (SAS) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755538.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286791	ENST00000755538.1		n.391-14077C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4105 AN: 152164 Hom.: 70 Cov.: 33

Gnomad AFR AF: 0.00664

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0269 AC: 4103 AN: 152282 Hom.: 70 Cov.: 33 AF XY: 0.0267 AC XY: 1986 AN XY: 74466

African (AFR) AF: 0.00662 AC: 275 AN: 41558

American (AMR) AF: 0.0171 AC: 261 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0642 AC: 310 AN: 4826

European-Finnish (FIN) AF: 0.0281 AC: 298 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0398 AC: 2710 AN: 68024

Other (OTH) AF: 0.0298 AC: 63 AN: 2112

Alfa AF: 0.0290 Hom.: 28

Bravo AF: 0.0236

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.39
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3851660; hg19: chr12-127723932; COSMIC: COSV107991108;