chr6-143001291-C-T

Variant names:

• chr6-143001291-C-T
• rs10484586
• ENST00000419957.6:n.1377+20375G>A

Variant summary

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

The ENST00000419957.6(LINC01277):​n.1377+20375G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 152,278 control chromosomes in the GnomAD database, including 315 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 0.053 (315 hom., cov: 32)
• Consequence: LINC01277 ENST00000419957.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419957.6. 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
	LINC01277	NR_038987.1		n.882+20375G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01277	ENST00000419957.6	TSL:2	n.1377+20375G>A		intron	N/A
	LINC01277	ENST00000446115.2	TSL:3	n.408-15161G>A		intron	N/A
	LINC01277	ENST00000653679.2		n.361-15161G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 8006 AN: 152160 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0526 AC: 8009 AN: 152278 Hom.: 315 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74446

African (AFR) AF: 0.0119 AC: 495 AN: 41560

American (AMR) AF: 0.0361 AC: 552 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3470

East Asian (EAS) AF: 0.0528 AC: 274 AN: 5186

South Asian (SAS) AF: 0.0536 AC: 259 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1360 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0708 AC: 4816 AN: 68024

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0639 Hom.: 197

Bravo AF: 0.0447

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10484586; hg19: chr6-143322428;