12-102681664-A-T

Variant names:

• chr12-102681664-A-T
• rs1353761
• ENST00000737486.1:n.122-8442A>T

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.122-8442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,050 control chromosomes in the GnomAD database, including 6,136 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 0.25 (6136 hom., cov: 31)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.27
• Publications: 4 publications found

Genes affected

ENSG00000296233 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737486.1. 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
	ENSG00000296233	ENST00000737486.1		n.122-8442A>T		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.122-8442A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38659 AN: 151932 Hom.: 6135 Cov.: 31

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.254 AC: 38661 AN: 152050 Hom.: 6136 Cov.: 31 AF XY: 0.255 AC XY: 18928 AN XY: 74324

African (AFR) AF: 0.0635 AC: 2638 AN: 41516

American (AMR) AF: 0.339 AC: 5182 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3300 AN: 10572

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23217 AN: 67910

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.195 Hom.: 484

Bravo AF: 0.248

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs1353761; hg19: chr12-103075442;