rs4145199

Positions:

• chr6-40384102-G-A
• chr6-40384102-G-C

Variant summary

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

The ENST00000373171.3(LINC00951):​n.3093C>T 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 0.864 in 152,178 control chromosomes in the GnomAD database, including 56,970 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 0.86 (56970 hom., cov: 32)
• Consequence: LINC00951 ENST00000373171.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

LINC00951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40384102G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00951	ENST00000373171.3	n.3093C>T		non_coding_transcript_exon_variant	1/4	2
TDRG1	ENST00000664585.1	n.718-2395G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131340 AN: 152060 Hom.: 56934 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.864 AC: 131429 AN: 152178 Hom.: 56970 Cov.: 32 AF XY: 0.859 AC XY: 63880 AN XY: 74408

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.880

Alfa AF: 0.890 Hom.: 118898

Bravo AF: 0.863

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4145199; hg19: chr6-40351841;