chr2-62486398-C-T

Position:

• chr2-62486398-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_024452749.2(TMEM17):​c.318+16039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,090 control chromosomes in the GnomAD database, including 4,922 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 0.25 (4922 hom., cov: 32)
• Consequence: TMEM17 XM_024452749.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

Genes affected

TMEM17 (HGNC:26623): (transmembrane protein 17) Involved in non-motile cilium assembly. Predicted to be located in ciliary membrane. Predicted to be part of MKS complex. Predicted to be active in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM17	XM_024452749.2	c.318+16039G>A		intron_variant			XP_024308517.1
TMEM17	XM_011532693.3	c.319-3650G>A		intron_variant			XP_011530995.1
TMEM17	XM_011532694.3	c.318+16039G>A		intron_variant			XP_011530996.1
		n.62486398C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37897 AN: 151972 Hom.: 4919 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.249 AC: 37941 AN: 152090 Hom.: 4922 Cov.: 32 AF XY: 0.249 AC XY: 18499 AN XY: 74332

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.220

Alfa AF: 0.225 Hom.: 7994

Bravo AF: 0.248

Asia WGS AF: 0.198 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6545946; hg19: chr2-62713533;