rs10499196

Positions:

• chr6-137698529-C-A

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+24405C>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 0.09 in 151,800 control chromosomes in the GnomAD database, including 675 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 0.090 (675 hom., cov: 31)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

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

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901411	XR_007059789.1	n.164-148C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+24405C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000637996.1	n.161-148C>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+9840C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13635 AN: 151532 Hom.: 671 Cov.: 31

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.0882

GnomAD4 exome AF: 0.122 AC: 19 AN: 156 Hom.: 0 AF XY: 0.0978 AC XY: 9 AN XY: 92

Gnomad4 EAS exome AF: 0.116

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.0900 AC: 13650 AN: 151644 Hom.: 675 Cov.: 31 AF XY: 0.0909 AC XY: 6729 AN XY: 74052

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.0868

Alfa AF: 0.0972 Hom.: 384

Bravo AF: 0.0881

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499196; hg19: chr6-138019666;