8-52011249-A-G

Variant names:

• chr8-52011249-A-G
• rs10104090
• ENST00000521188.1:n.114-11167A>G

Variant summary

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

The ENST00000521188.1(PCMTD1-DT):​n.114-11167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,206 control chromosomes in the GnomAD database, including 2,125 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 (2125 hom., cov: 33)
• Consequence: PCMTD1-DT ENST00000521188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901944	XR_007060910.1	n.116-11167A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCMTD1-DT	ENST00000521188.1	n.114-11167A>G		intron_variant	Intron 1 of 1	3
PCMTD1-DT	ENST00000702548.1	n.116-11167A>G		intron_variant	Intron 1 of 1
PCMTD1-DT	ENST00000762741.1	n.320-11167A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21241 AN: 152088 Hom.: 2113 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.140 AC: 21291 AN: 152206 Hom.: 2125 Cov.: 33 AF XY: 0.139 AC XY: 10363 AN XY: 74436

African (AFR) AF: 0.253 AC: 10523 AN: 41514

American (AMR) AF: 0.157 AC: 2399 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1843 AN: 5154

South Asian (SAS) AF: 0.132 AC: 634 AN: 4818

European-Finnish (FIN) AF: 0.0434 AC: 461 AN: 10626

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4793 AN: 68028

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0982 Hom.: 3765

Bravo AF: 0.156

Asia WGS AF: 0.228 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.24
PhyloP100		-1.8
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: rs10104090; hg19: chr8-52923809;