6-137701403-T-G

Variant names:

• chr6-137701403-T-G
• rs647108
• ENST00000635999.1:n.433+27279T>G

Variant summary

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

The ENST00000646621.1(LINC03004):​n.601+12714T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,056 control chromosomes in the GnomAD database, including 18,558 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 0.48 (18558 hom., cov: 32)
• Consequence: LINC03004 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 9 publications found

Genes affected

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

ENSG00000303318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 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+27279T>G		intron	N/A
	LINC03004	ENST00000646621.1		n.601+12714T>G		intron	N/A
	ENSG00000303318	ENST00000793597.1		n.305-1874A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73332 AN: 151938 Hom.: 18550 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.482 AC: 73366 AN: 152056 Hom.: 18558 Cov.: 32 AF XY: 0.486 AC XY: 36133 AN XY: 74330

African (AFR) AF: 0.613 AC: 25435 AN: 41476

American (AMR) AF: 0.443 AC: 6765 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4129 AN: 5176

South Asian (SAS) AF: 0.434 AC: 2091 AN: 4816

European-Finnish (FIN) AF: 0.472 AC: 4987 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27203 AN: 67974

Other (OTH) AF: 0.483 AC: 1020 AN: 2112

Alfa AF: 0.425 Hom.: 57672

Bravo AF: 0.486

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.76
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs647108; hg19: chr6-138022540; COSMIC: COSV68432206;