rs4145199

Variant names:

• chr6-40384102-G-A
• rs4145199
• ENST00000373171.3:n.3093C>T

Your query was ambiguous. Multiple possible variants found:

• 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:48662): (long intergenic non-protein coding RNA 951)

TDRG1 (HGNC:43642): (testis development related 1) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00951	ENST00000373171.3	n.3093C>T		non_coding_transcript_exon_variant	Exon 1 of 4	2
TDRG1	ENST00000664585.1	n.718-2395G>A		intron_variant	Intron 2 of 3

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;