ENST00000635999.1:n.434-2192G>A

Variant names:

• chr6-137761625-G-A
• rs946227
• ENST00000635999.1:n.434-2192G>A

Variant summary

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

The ENST00000635999.1(LINC03004):​n.434-2192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,074 control chromosomes in the GnomAD database, including 6,391 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 0.26 (6391 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 8 publications found

Genes affected

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

LINC02539 (HGNC:53572): (long intergenic non-protein coding RNA 2539)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.434-2192G>A		intron	N/A
	LINC02539	ENST00000645996.1		n.213+23107C>T		intron	N/A
	LINC02539	ENST00000821781.1		n.278+18515C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39389 AN: 151956 Hom.: 6393 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.259 AC: 39381 AN: 152074 Hom.: 6391 Cov.: 32 AF XY: 0.258 AC XY: 19157 AN XY: 74330

African (AFR) AF: 0.0717 AC: 2975 AN: 41494

American (AMR) AF: 0.226 AC: 3458 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3464

East Asian (EAS) AF: 0.260 AC: 1347 AN: 5172

South Asian (SAS) AF: 0.189 AC: 909 AN: 4822

European-Finnish (FIN) AF: 0.379 AC: 3991 AN: 10540

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

European-Non Finnish (NFE) AF: 0.365 AC: 24840 AN: 67976

Other (OTH) AF: 0.261 AC: 550 AN: 2110

Alfa AF: 0.300 Hom.: 13139

Bravo AF: 0.241

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
DANN	Benign	0.85
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs946227; hg19: chr6-138082762;