rs946227

Variant names:

• chr6-137761625-G-A
• rs946227
• ENST00000635999.1:n.434-2192G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-137761625-G-A
• chr6-137761625-G-C
• chr6-137761625-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.434-2192G>A		intron_variant	Intron 2 of 2	5
LINC02539	ENST00000645996.1	n.213+23107C>T		intron_variant	Intron 2 of 2

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;