rs946227

chr6-137761625-G-Achr6-137761625-G-T

Variant summary

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

The ENST00000635999.1(LINC03004):n.434-2192G>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 0.259 in 152,074 control chromosomes in the GnomAD database, including 6,391 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 0.26 (6391 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

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

LINC02539 (HGNC:53572): (long intergenic non-protein coding RNA 2539)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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.434-2192G>A		intron_variant, non_coding_transcript_variant		5
LINC02539	ENST00000645996.1	n.213+23107C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39389 AN: 151956 Hom.: 6393 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.259 AC: 39381 AN: 152074 Hom.: 6391 Cov.: 32 AF XY: 0.258 AC XY: 19157 AN XY: 74330

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.261

Alfa AF: 0.334 Hom.: 8735

Bravo AF: 0.241

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.64
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs946227; hg19: chr6-138082762;