12-23050945-G-T

Variant names:

• chr12-23050945-G-T
• rs8181738
• ENST00000538317.6:n.858-3046G>T

Variant summary

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

The ENST00000538317.6(LINC02955):​n.858-3046G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,870 control chromosomes in the GnomAD database, including 17,467 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 0.45 (17467 hom., cov: 32)
• Consequence: LINC02955 ENST00000538317.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 1 publications found

Genes affected

LINC02955 (HGNC:55973): (long intergenic non-protein coding RNA 2955)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538317.6. 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
	LINC02955	NR_187500.1		n.1116-3046G>T		intron	N/A
	LINC02955	NR_187501.1		n.960-3046G>T		intron	N/A
	LINC02955	NR_187503.1		n.1090-3046G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000538317.6	TSL:4	n.858-3046G>T		intron	N/A
	LINC02955	ENST00000540895.6	TSL:2	n.607-3046G>T		intron	N/A
	LINC02955	ENST00000540994.1	TSL:3	n.235-3046G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68129 AN: 151752 Hom.: 17477 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.449 AC: 68122 AN: 151870 Hom.: 17467 Cov.: 32 AF XY: 0.448 AC XY: 33236 AN XY: 74200

African (AFR) AF: 0.198 AC: 8234 AN: 41482

American (AMR) AF: 0.442 AC: 6733 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1770 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1791 AN: 5142

South Asian (SAS) AF: 0.438 AC: 2113 AN: 4828

European-Finnish (FIN) AF: 0.569 AC: 5992 AN: 10532

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 39957 AN: 67874

Other (OTH) AF: 0.466 AC: 982 AN: 2106

Alfa AF: 0.535 Hom.: 11204

Bravo AF: 0.422

Asia WGS AF: 0.357 AC: 1237 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs8181738; hg19: chr12-23203879;