rs9321627

Variant names:

• chr6-137701911-G-A
• rs9321627
• ENST00000635999.1:n.433+27787G>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+27787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,160 control chromosomes in the GnomAD database, including 3,619 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 0.19 (3619 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 10 publications found

Genes affected

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

ENSG00000303318 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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+27787G>A		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000646621.1	n.601+13222G>A		intron_variant	Intron 4 of 4
ENSG00000303318	ENST00000793597.1	n.305-2382C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28763 AN: 152042 Hom.: 3621 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.189 AC: 28747 AN: 152160 Hom.: 3619 Cov.: 32 AF XY: 0.198 AC XY: 14755 AN XY: 74394

African (AFR) AF: 0.0406 AC: 1688 AN: 41552

American (AMR) AF: 0.251 AC: 3832 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2735 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4816

European-Finnish (FIN) AF: 0.305 AC: 3227 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14665 AN: 67986

Other (OTH) AF: 0.205 AC: 433 AN: 2112

Alfa AF: 0.211 Hom.: 847

Bravo AF: 0.177

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.83
DANN	Benign	0.79
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs9321627; hg19: chr6-138023048; COSMIC: COSV68432211;