rs17212214

Variant names:

• chr8-51918582-T-G
• rs17212214
• ENST00000423716.1:n.198+18736T>G

Variant summary

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

The ENST00000423716.1(PCMTD1-DT):​n.198+18736T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,196 control chromosomes in the GnomAD database, including 2,254 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 0.16 (2254 hom., cov: 32)
• Consequence: PCMTD1-DT ENST00000423716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 1 publications found

Genes affected

PCMTD1-DT (HGNC:55791): (PCMTD1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCMTD1-DT	NR_189277.1	n.656+5402T>G		intron_variant	Intron 2 of 2
PCMTD1-DT	NR_189278.1	n.532+18736T>G		intron_variant	Intron 1 of 1
PCMTD1-DT	NR_189279.1	n.656+5402T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCMTD1-DT	ENST00000423716.1	n.198+18736T>G		intron_variant	Intron 1 of 1	2
PCMTD1-DT	ENST00000518942.3	n.656+5402T>G		intron_variant	Intron 2 of 2	3
PCMTD1-DT	ENST00000656129.1	n.579+18736T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23597 AN: 152078 Hom.: 2249 Cov.: 32

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.155 AC: 23613 AN: 152196 Hom.: 2254 Cov.: 32 AF XY: 0.159 AC XY: 11859 AN XY: 74372

African (AFR) AF: 0.0588 AC: 2443 AN: 41550

American (AMR) AF: 0.119 AC: 1825 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.164 AC: 845 AN: 5156

South Asian (SAS) AF: 0.151 AC: 728 AN: 4816

European-Finnish (FIN) AF: 0.265 AC: 2799 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13789 AN: 68012

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.182 Hom.: 7414

Bravo AF: 0.139

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17212214; hg19: chr8-52831142;