9-68614263-A-G

Variant names:

• chr9-68614263-A-G
• rs7864204
• ENST00000413269.3:n.461-11378A>G

Variant summary

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

The ENST00000413269.3(TMEM252-DT):​n.461-11378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,848 control chromosomes in the GnomAD database, including 28,815 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 0.61 (28815 hom., cov: 31)
• Consequence: TMEM252-DT ENST00000413269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 9 publications found

Genes affected

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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413269.3. 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
	TMEM252-DT	NR_187592.1		n.472-11378A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM252-DT	ENST00000413269.3	TSL:1	n.461-11378A>G		intron	N/A
	LINC01506	ENST00000762443.1		n.355+20198T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92721 AN: 151730 Hom.: 28811 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.611 AC: 92769 AN: 151848 Hom.: 28815 Cov.: 31 AF XY: 0.610 AC XY: 45271 AN XY: 74190

African (AFR) AF: 0.548 AC: 22704 AN: 41394

American (AMR) AF: 0.503 AC: 7659 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2195 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2127 AN: 5142

South Asian (SAS) AF: 0.645 AC: 3098 AN: 4804

European-Finnish (FIN) AF: 0.703 AC: 7398 AN: 10526

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

European-Non Finnish (NFE) AF: 0.668 AC: 45385 AN: 67972

Other (OTH) AF: 0.623 AC: 1311 AN: 2104

Alfa AF: 0.632 Hom.: 65818

Bravo AF: 0.587

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7864204; hg19: chr9-71229179;