rs10499194

chr6-137681500-C-T

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+7376C>T 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 0.237 in 151,452 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 29)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 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+7376C>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.439-5594C>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.415-5594C>T		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.393-5594C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35944 AN: 151332 Hom.: 4586 Cov.: 29

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.237 AC: 35954 AN: 151452 Hom.: 4590 Cov.: 29 AF XY: 0.235 AC XY: 17420 AN XY: 73982

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0389

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.239

Alfa AF: 0.259 Hom.: 530

Bravo AF: 0.242

Asia WGS AF: 0.148 AC: 517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.9
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499194; hg19: chr6-138002637;