6-40360639-A-G

Variant names:

• chr6-40360639-A-G
• rs2038868
• ENST00000447315.2:n.87-1158T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447315.2(LINC00951):​n.87-1158T>C variant causes a intron 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 ENST00000447315.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00951	ENST00000447315.2	n.87-1158T>C		intron_variant	Intron 1 of 1	1
LINC00951	ENST00000373171.4	n.8691-7110T>C		intron_variant	Intron 1 of 3	2
TDRG1	ENST00000448559.5	n.138-18643A>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.0168 AC: 699 AN: 41566

American (AMR) AF: 0.0663 AC: 1015 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.114 AC: 588 AN: 5178

South Asian (SAS) AF: 0.00602 AC: 29 AN: 4820

European-Finnish (FIN) AF: 0.0812 AC: 861 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00398 AC: 271 AN: 68026

Other (OTH) AF: 0.0223 AC: 47 AN: 2112

Alfa AF: 0.0121 Hom.: 94

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
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs2038868; hg19: chr6-40328378;