6-137681500-C-T

Variant names:

• chr6-137681500-C-T
• rs10499194
• ENST00000635999.1:n.433+7376C>T

Variant summary

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

The ENST00000646621.1(LINC03004):​n.415-5594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,452 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 29)
• Consequence: LINC03004 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 135 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646621.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.433+7376C>T		intron	N/A
	LINC03004	ENST00000638039.2	TSL:5	n.439-5594C>T		intron	N/A
	LINC03004	ENST00000646621.1		n.415-5594C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35944 AN: 151332 Hom.: 4586 Cov.: 29

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.237 AC: 35954 AN: 151452 Hom.: 4590 Cov.: 29 AF XY: 0.235 AC XY: 17420 AN XY: 73982

African (AFR) AF: 0.171 AC: 7065 AN: 41232

American (AMR) AF: 0.287 AC: 4350 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3468

East Asian (EAS) AF: 0.0389 AC: 201 AN: 5164

South Asian (SAS) AF: 0.258 AC: 1230 AN: 4774

European-Finnish (FIN) AF: 0.224 AC: 2346 AN: 10480

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18577 AN: 67866

Other (OTH) AF: 0.239 AC: 503 AN: 2108

Alfa AF: 0.256 Hom.: 14148

Bravo AF: 0.242

Asia WGS AF: 0.148 AC: 517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.65
PhyloP100		-0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10499194;

hg19: chr6-138002637;