rs10490034

Variant names:

• chr2-229053305-A-G
• rs10490034
• NM_001100818.2:c.178-27197T>C

Variant summary

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

The NM_001100818.2(PID1):​c.178-27197T>C 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 152,188 control chromosomes in the GnomAD database, including 2,167 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 (2167 hom., cov: 33)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

Genes affected

PID1 (HGNC:26084): (phosphotyrosine interaction domain containing 1) Involved in several processes, including mitochondrion morphogenesis; negative regulation of phosphate metabolic process; and positive regulation of macromolecule metabolic process. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PID1	NM_001100818.2	c.178-27197T>C		intron_variant	Intron 2 of 2	ENST00000392055.8	NP_001094288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PID1	ENST00000392055.8	c.178-27197T>C		intron_variant	Intron 2 of 2	2	NM_001100818.2	ENSP00000375908.3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21287 AN: 152070 Hom.: 2157 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.140 AC: 21329 AN: 152188 Hom.: 2167 Cov.: 33 AF XY: 0.144 AC XY: 10709 AN XY: 74404

African (AFR) AF: 0.265 AC: 11017 AN: 41498

American (AMR) AF: 0.194 AC: 2962 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.139 AC: 719 AN: 5172

South Asian (SAS) AF: 0.121 AC: 585 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4234 AN: 68022

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.100 Hom.: 1621

Bravo AF: 0.152

Asia WGS AF: 0.173 AC: 600 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	18
DANN	Benign	0.83
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10490034; hg19: chr2-229918021;