rs6545946

Variant names:

• chr2-62486398-C-T
• rs6545946
• XM_024452749.2:c.318+16039G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000807688.1(ENSG00000228541):​n.292-14864C>T 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: ENSG00000228541 ENST00000807688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 25 publications found

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]

ENSG00000228541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807688.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228541	ENST00000807688.1		n.292-14864C>T		intron	N/A
	ENSG00000228541	ENST00000807713.1		n.270+7762C>T		intron	N/A
	ENSG00000228541	ENST00000807714.1		n.167-14864C>T		intron	N/A

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

African (AFR) AF: 0.319 AC: 13212 AN: 41470

American (AMR) AF: 0.213 AC: 3251 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3472

East Asian (EAS) AF: 0.157 AC: 812 AN: 5182

South Asian (SAS) AF: 0.229 AC: 1101 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2936 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15188 AN: 67982

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.229 Hom.: 17418

Bravo AF: 0.248

Asia WGS AF: 0.198 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	12
DANN	Benign	0.52
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6545946; hg19: chr2-62713533;