rs9507041

Positions:

• chr13-23170240-C-T

Variant summary

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

The ENST00000414345.2(LINC00362):​n.47-188G>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 0.122 in 152,152 control chromosomes in the GnomAD database, including 1,185 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 0.12 (1185 hom., cov: 33)
• Consequence: LINC00362 ENST00000414345.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850

Genes affected

LINC00362 (HGNC:42682): (long intergenic non-protein coding RNA 362)

SGCG (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 = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00362	XR_007063718.1	n.322-188G>A		intron_variant, non_coding_transcript_variant
SGCG	NM_001378244.1	c.54+9594C>T		intron_variant			NP_001365173.1
SGCG	XM_047430542.1	c.54+9594C>T		intron_variant			XP_047286498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00362	ENST00000414345.2	n.47-188G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18553 AN: 152034 Hom.: 1186 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.122 AC: 18562 AN: 152152 Hom.: 1185 Cov.: 33 AF XY: 0.120 AC XY: 8921 AN XY: 74388

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0978

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.139

Alfa AF: 0.117 Hom.: 2362

Bravo AF: 0.128

Asia WGS AF: 0.116 AC: 405 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	0.45
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: rs9507041; hg19: chr13-23744379;