12-127912927-A-G

Variant names:

• chr12-127912927-A-G
• rs4034627
• ENST00000741352.1:n.316+27647T>C

Variant summary

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

The ENST00000741352.1(LINC00508):​n.316+27647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,150 control chromosomes in the GnomAD database, including 50,625 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 0.79 (50625 hom., cov: 31)
• Consequence: LINC00508 ENST00000741352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 10 publications found

Genes affected

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00508	NR_126452.2	n.311+27647T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00508	ENST00000741352.1	n.316+27647T>C		intron_variant	Intron 3 of 3
LINC00508	ENST00000741353.1	n.283+27647T>C		intron_variant	Intron 3 of 4
LINC00508	ENST00000741354.1	n.434+27647T>C		intron_variant	Intron 2 of 2
LINC00508	ENST00000741355.1	n.285+27647T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119683 AN: 152032 Hom.: 50599 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.787 AC: 119747 AN: 152150 Hom.: 50625 Cov.: 31 AF XY: 0.791 AC XY: 58882 AN XY: 74400

African (AFR) AF: 0.464 AC: 19226 AN: 41468

American (AMR) AF: 0.887 AC: 13571 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3345 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2841 AN: 5158

South Asian (SAS) AF: 0.923 AC: 4438 AN: 4806

European-Finnish (FIN) AF: 0.950 AC: 10079 AN: 10612

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63418 AN: 68020

Other (OTH) AF: 0.827 AC: 1743 AN: 2108

Alfa AF: 0.882 Hom.: 31405

Bravo AF: 0.765

Asia WGS AF: 0.728 AC: 2529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.49
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4034627; hg19: chr12-128397472;