rs508214

Positions:

• chr6-137692528-A-G
• chr6-137692528-A-T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+18404A>G 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 0.656 in 152,178 control chromosomes in the GnomAD database, including 33,286 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 0.66 (33286 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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.433+18404A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+3839A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99817 AN: 152060 Hom.: 33250 Cov.: 33

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.656 AC: 99900 AN: 152178 Hom.: 33286 Cov.: 33 AF XY: 0.656 AC XY: 48839 AN XY: 74410

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.655

Alfa AF: 0.632 Hom.: 5170

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs508214; hg19: chr6-138013665; COSMIC: COSV60285704;