rs4896295

Variant names:

• chr6-137676195-G-C
• rs4896295
• ENST00000635999.1:n.433+2071G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635999.1(LINC03004):​n.433+2071G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,010 control chromosomes in the GnomAD database, including 4,743 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 (4743 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+2071G>C		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.1	n.438+2071G>C		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.414+2071G>C		intron_variant	Intron 2 of 4
LINC03004	ENST00000666119.1	n.392+2071G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37041 AN: 151892 Hom.: 4739 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.244 AC: 37042 AN: 152010 Hom.: 4743 Cov.: 32 AF XY: 0.242 AC XY: 18008 AN XY: 74296

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0974

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.246

Alfa AF: 0.255 Hom.: 643

Bravo AF: 0.250

Asia WGS AF: 0.155 AC: 537 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896295; hg19: chr6-137997332;