6-142976370-T-G

Variant names:

• chr6-142976370-T-G
• rs6939141
• ENST00000419957.6:n.1378-8929A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419957.6(LINC01277):​n.1378-8929A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,226 control chromosomes in the GnomAD database, including 1,866 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 0.15 (1866 hom., cov: 32)
• Consequence: LINC01277 ENST00000419957.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

LINC01277 (HGNC:50334): (long intergenic non-protein coding RNA 1277)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01277	NR_038987.1	n.883-8929A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01277	ENST00000419957.6	n.1378-8929A>C		intron_variant	Intron 2 of 2	2
LINC01277	ENST00000446115.2	n.494-8929A>C		intron_variant	Intron 3 of 3	3
LINC01277	ENST00000657620.1	n.560-8929A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22167 AN: 152108 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.146 AC: 22211 AN: 152226 Hom.: 1866 Cov.: 32 AF XY: 0.147 AC XY: 10947 AN XY: 74434

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.134

Alfa AF: 0.138 Hom.: 827

Bravo AF: 0.148

Asia WGS AF: 0.204 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6939141; hg19: chr6-143297507;