rs1015213

Variant names:

• chr8-51974981-C-T
• rs1015213
• ENST00000521188.1:n.113+13411C>T

Variant summary

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

The ENST00000521188.1(PCMTD1-DT):​n.113+13411C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,086 control chromosomes in the GnomAD database, including 2,200 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 0.14 (2200 hom., cov: 32)
• Consequence: PCMTD1-DT ENST00000521188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 41 publications found

Genes affected

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

LOC124901944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521188.1. 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
	PCMTD1-DT	ENST00000521188.1	TSL:3	n.113+13411C>T		intron	N/A
	PCMTD1-DT	ENST00000702548.1		n.115+1246C>T		intron	N/A
	PCMTD1-DT	ENST00000762741.1		n.320-47435C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20515 AN: 151968 Hom.: 2194 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20552 AN: 152086 Hom.: 2200 Cov.: 32 AF XY: 0.131 AC XY: 9728 AN XY: 74360

African (AFR) AF: 0.295 AC: 12215 AN: 41400

American (AMR) AF: 0.0800 AC: 1224 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3470

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5180

South Asian (SAS) AF: 0.0893 AC: 431 AN: 4824

European-Finnish (FIN) AF: 0.0377 AC: 399 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5541 AN: 68016

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.0968 Hom.: 3435

Bravo AF: 0.143

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.68
PhyloP100		-1.1
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: rs1015213; hg19: chr8-52887541;