rs7867860

Positions:

• chr9-105997199-C-T

Variant summary

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

The ENST00000637185.1(LINC01505):​n.559+3331C>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 0.178 in 152,090 control chromosomes in the GnomAD database, including 2,509 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 0.18 (2509 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

LOC107987108 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987108	XR_007061713.1	n.2032+21068C>T		intron_variant, non_coding_transcript_variant
LOC107987108	XR_001746870.2	n.2032+21068C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+3331C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27011 AN: 151972 Hom.: 2508 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.178 AC: 27034 AN: 152090 Hom.: 2509 Cov.: 32 AF XY: 0.176 AC XY: 13119 AN XY: 74340

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.185

Alfa AF: 0.164 Hom.: 4419

Bravo AF: 0.183

Asia WGS AF: 0.148 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
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: rs7867860; hg19: chr9-108759480;