rs11752942

Positions:

• chr6-40354019-A-G

Variant summary

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

The NR_038887.1(LINC00951):​n.1988T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,148 control chromosomes in the GnomAD database, including 18,038 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 0.46 (18038 hom., cov: 32)
• Consequence: LINC00951 NR_038887.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

LINC00951 (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 (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00951	NR_038887.1	n.1988T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00951	ENST00000700329.1	n.2534T>C		non_coding_transcript_exon_variant	1/3
LINC00951	ENST00000373171.3	n.8691-490T>C		intron_variant		2
TDRG1	ENST00000448559.5	n.137+13418A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70470 AN: 152030 Hom.: 18032 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.463 AC: 70509 AN: 152148 Hom.: 18038 Cov.: 32 AF XY: 0.466 AC XY: 34689 AN XY: 74378

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.489

Alfa AF: 0.511 Hom.: 5424

Bravo AF: 0.449

Asia WGS AF: 0.487 AC: 1696 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	0.20
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752942; hg19: chr6-40321758;