ENST00000635999.1:n.433+10254A>G

Variant names:

• chr6-137684378-A-G
• rs17264332
• ENST00000635999.1:n.433+10254A>G

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+10254A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,120 control chromosomes in the GnomAD database, including 2,102 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 0.16 (2102 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 48 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 (NFE) allele frequency at 95% confidence interval = 0.205 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.433+10254A>G		intron	N/A
	LINC03004	ENST00000638039.2	TSL:5	n.439-2716A>G		intron	N/A
	LINC03004	ENST00000646621.1		n.415-2716A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24021 AN: 152002 Hom.: 2100 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 24030 AN: 152120 Hom.: 2102 Cov.: 33 AF XY: 0.154 AC XY: 11419 AN XY: 74370

African (AFR) AF: 0.110 AC: 4556 AN: 41508

American (AMR) AF: 0.125 AC: 1916 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.104 AC: 504 AN: 4826

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10572

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14143 AN: 67966

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.181 Hom.: 3975

Bravo AF: 0.152

Asia WGS AF: 0.0500 AC: 175 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	1.9
DANN	Benign	0.83
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17264332; hg19: chr6-138005515;