rs2038868

Positions:

• chr6-40360639-A-G

Variant summary

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

The ENST00000373171.3(LINC00951):​n.8691-7110T>C 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 0.0231 in 152,288 control chromosomes in the GnomAD database, including 124 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 0.023 (124 hom., cov: 32)
• Consequence: LINC00951 ENST00000373171.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973

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 (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00951	ENST00000373171.3	n.8691-7110T>C		intron_variant, non_coding_transcript_variant		2
TDRG1	ENST00000451810.3	n.493-18643A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3503 AN: 152170 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00398

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0231 AC: 3521 AN: 152288 Hom.: 124 Cov.: 32 AF XY: 0.0274 AC XY: 2041 AN XY: 74472

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.00398

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0137 Hom.: 9

Bravo AF: 0.0241

Asia WGS AF: 0.0590 AC: 204 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	3.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038868; hg19: chr6-40328378;