rs4896295

Variant names:

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

Variant summary

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

The ENST00000646621.1(LINC03004):​n.414+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 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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+2071G>C		intron	N/A
	LINC03004	ENST00000638039.2	TSL:5	n.438+2071G>C		intron	N/A
	LINC03004	ENST00000646621.1		n.414+2071G>C		intron	N/A

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

African (AFR) AF: 0.188 AC: 7781 AN: 41454

American (AMR) AF: 0.291 AC: 4450 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.0974 AC: 504 AN: 5176

South Asian (SAS) AF: 0.257 AC: 1243 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2359 AN: 10548

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18550 AN: 67944

Other (OTH) AF: 0.246 AC: 519 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.68
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4896295;

hg19: chr6-137997332;