rs1409375

Variant names:

• chr2-229053326-T-C
• rs1409375
• NM_001100818.2:c.178-27218A>G

Variant summary

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

The NM_001100818.2(PID1):​c.178-27218A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,082 control chromosomes in the GnomAD database, including 7,731 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 0.30 (7731 hom., cov: 33)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 1 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PID1	NM_001100818.2	c.178-27218A>G		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.178-27218A>G		intron_variant	Intron 2 of 2	2	NM_001100818.2	ENSP00000375908.3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45627 AN: 151962 Hom.: 7734 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.300 AC: 45609 AN: 152082 Hom.: 7731 Cov.: 33 AF XY: 0.299 AC XY: 22248 AN XY: 74328

African (AFR) AF: 0.142 AC: 5901 AN: 41518

American (AMR) AF: 0.326 AC: 4983 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2716 AN: 5166

South Asian (SAS) AF: 0.309 AC: 1489 AN: 4826

European-Finnish (FIN) AF: 0.314 AC: 3318 AN: 10564

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25021 AN: 67966

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.340 Hom.: 1161

Bravo AF: 0.296

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		-0.81
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: rs1409375; hg19: chr2-229918042;