rs6920220

Variant names:

• chr6-137685367-G-A
• rs6920220
• ENST00000635999.1:n.433+11243G>A

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+11243G>A 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 152,052 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 244 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=-0.78).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+11243G>A		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2	n.439-1727G>A		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.415-1727G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.110 AC: 4557 AN: 41498

American (AMR) AF: 0.125 AC: 1915 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5176

South Asian (SAS) AF: 0.106 AC: 510 AN: 4824

European-Finnish (FIN) AF: 0.178 AC: 1874 AN: 10544

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

European-Non Finnish (NFE) AF: 0.208 AC: 14146 AN: 67960

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.187 Hom.: 12296

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6920220; hg19: chr6-138006504;