rs4896295

chr6-137676195-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+2071G>C		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.438+2071G>C		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.414+2071G>C		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.392+2071G>C		intron_variant, non_coding_transcript_variant

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;