rs6920220

chr6-137685367-G-A

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+11243G>A 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 0.158 in 152,052 control chromosomes in the GnomAD database, including 2,104 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 (2104 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+11243G>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.439-1727G>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.415-1727G>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.393-1727G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24038 AN: 151934 Hom.: 2102 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.158 AC: 24050 AN: 152052 Hom.: 2104 Cov.: 32 AF XY: 0.154 AC XY: 11431 AN XY: 74320

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.161

Alfa AF: 0.190 Hom.: 5602

Bravo AF: 0.152

Asia WGS AF: 0.0520 AC: 184 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.3
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6920220; hg19: chr6-138006504;