chr6-137675662-T-A

Variant names:

• chr6-137675662-T-A
• rs9402914
• ENST00000635999.1:n.433+1538T>A

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+1538T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,064 control chromosomes in the GnomAD database, including 5,898 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 0.27 (5898 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 4 publications found

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+1538T>A		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2	n.438+1538T>A		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.414+1538T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41664 AN: 151946 Hom.: 5895 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.274 AC: 41674 AN: 152064 Hom.: 5898 Cov.: 32 AF XY: 0.283 AC XY: 21001 AN XY: 74332

African (AFR) AF: 0.252 AC: 10447 AN: 41484

American (AMR) AF: 0.292 AC: 4466 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2718 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1548 AN: 4822

European-Finnish (FIN) AF: 0.352 AC: 3716 AN: 10566

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17063 AN: 67978

Other (OTH) AF: 0.289 AC: 609 AN: 2106

Alfa AF: 0.151 Hom.: 309

Bravo AF: 0.269

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs9402914; hg19: chr6-137996799; COSMIC: COSV71077267;