12-126640834-C-T

Variant names:

• chr12-126640834-C-T
• rs2347306
• ENST00000541769.1:n.368+6536G>A

Variant summary

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

The ENST00000541769.1(LINC00944):​n.368+6536G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,284 control chromosomes in the GnomAD database, including 64,736 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 0.92 (64736 hom., cov: 33)
• Consequence: LINC00944 ENST00000541769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

Genes affected

LINC00944 (HGNC:48640): (long intergenic non-protein coding RNA 944)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000541769.1. 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
	LINC00944	ENST00000541769.1	TSL:5	n.368+6536G>A		intron	N/A
	LINC00944	ENST00000545853.2	TSL:3	n.280-30571G>A		intron	N/A
	LINC00944	ENST00000809141.1		n.262-30571G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140219 AN: 152166 Hom.: 64719 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.921 AC: 140282 AN: 152284 Hom.: 64736 Cov.: 33 AF XY: 0.922 AC XY: 68636 AN XY: 74464

African (AFR) AF: 0.863 AC: 35855 AN: 41544

American (AMR) AF: 0.930 AC: 14234 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3376 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4380 AN: 5176

South Asian (SAS) AF: 0.977 AC: 4711 AN: 4824

European-Finnish (FIN) AF: 0.936 AC: 9935 AN: 10618

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64815 AN: 68032

Other (OTH) AF: 0.926 AC: 1960 AN: 2116

Alfa AF: 0.932 Hom.: 10993

Bravo AF: 0.917

Asia WGS AF: 0.913 AC: 3174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2347306; hg19: chr12-127125380;