rs1320333

Positions:

• chr2-679179-C-T

Variant summary

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

The NR_183417.1(TMEM18-DT):​n.103-865C>T 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 0.0934 in 152,192 control chromosomes in the GnomAD database, including 648 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 0.093 (648 hom., cov: 32)
• Consequence: TMEM18-DT NR_183417.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

TMEM18-DT (HGNC:54481): (TMEM18 divergent transcript)

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 (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM18-DT	NR_183417.1	n.103-865C>T		intron_variant, non_coding_transcript_variant
TMEM18-DT	NR_183416.1	n.116-865C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM18-DT	ENST00000445418.1	n.289-865C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14204 AN: 152074 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.0934 AC: 14214 AN: 152192 Hom.: 648 Cov.: 32 AF XY: 0.0914 AC XY: 6801 AN XY: 74396

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0832

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0921

Alfa AF: 0.101 Hom.: 1119

Bravo AF: 0.0925

Asia WGS AF: 0.0670 AC: 232 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	2.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320333; hg19: chr2-679179;