chr6-40354019-A-G

Variant names:

• chr6-40354019-A-G
• rs11752942
• ENST00000700329.2:n.2534T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_038887.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00951	NR_038887.1		n.1988T>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00951	ENST00000700329.2		n.2534T>C		non_coding_transcript_exon	Exon 1 of 3
	LINC00951	ENST00000373171.4	TSL:2	n.8691-490T>C		intron	N/A
	TDRG1	ENST00000448559.5	TSL:2	n.137+13418A>G		intron	N/A

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

African (AFR) AF: 0.236 AC: 9816 AN: 41518

American (AMR) AF: 0.548 AC: 8367 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5166

South Asian (SAS) AF: 0.652 AC: 3138 AN: 4814

European-Finnish (FIN) AF: 0.536 AC: 5678 AN: 10600

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37921 AN: 67974

Other (OTH) AF: 0.489 AC: 1035 AN: 2116

Alfa AF: 0.446 Hom.: 6114

Bravo AF: 0.449

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11752942; hg19: chr6-40321758;