rs2051936

chr7-40970951-C-T

Variant summary

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

The NR_110831.1(LINC01450):n.567-2767G>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 0.229 in 151,992 control chromosomes in the GnomAD database, including 4,961 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 0.23 (4961 hom., cov: 33)
• Consequence: LINC01450 NR_110831.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

LINC01450 (HGNC:50792): (long intergenic non-protein coding RNA 1450)

SUGCT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01450	NR_110831.1	n.567-2767G>A		intron_variant, non_coding_transcript_variant
SUGCT	XR_007060157.1	n.1344-58073C>T		intron_variant, non_coding_transcript_variant
SUGCT	XR_007060158.1	n.1200-58073C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01450	ENST00000443406.1	n.567-2767G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34703 AN: 151874 Hom.: 4946 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.229 AC: 34764 AN: 151992 Hom.: 4961 Cov.: 33 AF XY: 0.231 AC XY: 17141 AN XY: 74322

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.211

Alfa AF: 0.181 Hom.: 595

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2051936; hg19: chr7-41010550;