rs536331

Variant names:

• chr6-137671912-T-C
• rs536331
• XR_943058.3:n.525A>G

Variant summary

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

The XR_943058.3(LOC105378018):​n.525A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,926 control chromosomes in the GnomAD database, including 15,331 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 0.45 (15331 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC105378018 XR_943058.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 7 publications found

Genes affected

LOC105378018 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378018	XR_943058.3	n.525A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC03004	NR_125867.1	n.95-108T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000642830.1	n.426-108T>C		intron_variant	Intron 4 of 6
LINC03004	ENST00000691587.2	n.314-108T>C		intron_variant	Intron 2 of 4
LINC03004	ENST00000692965.3	n.289-108T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67571 AN: 151808 Hom.: 15314 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.445 AC: 67612 AN: 151926 Hom.: 15331 Cov.: 32 AF XY: 0.438 AC XY: 32547 AN XY: 74230

African (AFR) AF: 0.532 AC: 22075 AN: 41456

American (AMR) AF: 0.440 AC: 6723 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1673 AN: 3448

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5176

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3631 AN: 10552

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28696 AN: 67898

Other (OTH) AF: 0.433 AC: 913 AN: 2108

Alfa AF: 0.439 Hom.: 10708

Bravo AF: 0.458

Asia WGS AF: 0.320 AC: 1110 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs536331; hg19: chr6-137993049; COSMIC: COSV71077366;