chr6-137697302-A-G

Variant names:

• chr6-137697302-A-G
• rs6917441
• ENST00000635999.1:n.433+23178A>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+8613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,132 control chromosomes in the GnomAD database, including 7,147 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 0.30 (7147 hom., cov: 33)
• Consequence: LINC03004 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 9 publications found

Genes affected

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

ENSG00000283265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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+23178A>G		intron	N/A
	ENSG00000283265	ENST00000637996.1	TSL:5	n.161-1375A>G		intron	N/A
	LINC03004	ENST00000646621.1		n.601+8613A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45799 AN: 152014 Hom.: 7149 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.301 AC: 45803 AN: 152132 Hom.: 7147 Cov.: 33 AF XY: 0.308 AC XY: 22923 AN XY: 74384

African (AFR) AF: 0.349 AC: 14469 AN: 41488

American (AMR) AF: 0.304 AC: 4643 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2775 AN: 5176

South Asian (SAS) AF: 0.317 AC: 1532 AN: 4828

European-Finnish (FIN) AF: 0.351 AC: 3719 AN: 10592

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16922 AN: 67968

Other (OTH) AF: 0.310 AC: 656 AN: 2114

Alfa AF: 0.266 Hom.: 17965

Bravo AF: 0.300

Asia WGS AF: 0.410 AC: 1426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs6917441; hg19: chr6-138018439;