rs2183737

Variant names:

• chr9-68626717-G-A
• rs2183737
• ENST00000413269.3:n.667+870G>A

Variant summary

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

The ENST00000413269.3(TMEM252-DT):​n.667+870G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,162 control chromosomes in the GnomAD database, including 4,479 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 0.13 (4479 hom., cov: 32)
• Consequence: TMEM252-DT ENST00000413269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 2 publications found

Genes affected

TMEM252-DT (HGNC:54377): (TMEM252 divergent transcript)

LOC105376071 (HGNC:):

LINC01506 (HGNC:51187): (long intergenic non-protein coding RNA 1506)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376071	XR_929902.3	n.773C>T		non_coding_transcript_exon_variant	Exon 3 of 3
TMEM252-DT	NR_187592.1	n.678+870G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM252-DT	ENST00000413269.3	n.667+870G>A		intron_variant	Intron 3 of 4	1
LINC01506	ENST00000762443.1	n.355+7744C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20248 AN: 152044 Hom.: 4465 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00953

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.133 AC: 20287 AN: 152162 Hom.: 4479 Cov.: 32 AF XY: 0.128 AC XY: 9509 AN XY: 74414

African (AFR) AF: 0.459 AC: 19021 AN: 41428

American (AMR) AF: 0.0538 AC: 823 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00892 AC: 43 AN: 4822

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10626

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00237 AC: 161 AN: 68016

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0701 Hom.: 641

Bravo AF: 0.153

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs2183737; hg19: chr9-71241633;