chr2-229038405-T-G

Variant names:

• chr2-229038405-T-G
• rs3845823
• NM_001100818.2:c.178-12297A>C

Variant summary

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

The NM_001330156.1(PID1):​c.277-12297A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,882 control chromosomes in the GnomAD database, including 26,106 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 0.58 (26106 hom., cov: 31)
• Consequence: PID1 NM_001330156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330156.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PID1	NM_001100818.2	MANE Select	c.178-12297A>C		intron	N/A	NP_001094288.1
	PID1	NM_001330156.1		c.277-12297A>C		intron	N/A	NP_001317085.1
	PID1	NM_017933.5		c.271-12297A>C		intron	N/A	NP_060403.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PID1	ENST00000392055.8	TSL:2 MANE Select	c.178-12297A>C		intron	N/A	ENSP00000375908.3
	PID1	ENST00000409462.1	TSL:1	c.31-12297A>C		intron	N/A	ENSP00000386826.1
	PID1	ENST00000354069.6	TSL:3	c.277-12297A>C		intron	N/A	ENSP00000283937.8

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88714 AN: 151764 Hom.: 26071 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.585 AC: 88811 AN: 151882 Hom.: 26106 Cov.: 31 AF XY: 0.580 AC XY: 43030 AN XY: 74222

African (AFR) AF: 0.646 AC: 26771 AN: 41414

American (AMR) AF: 0.577 AC: 8793 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1850 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3028 AN: 5154

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4804

European-Finnish (FIN) AF: 0.536 AC: 5663 AN: 10556

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38910 AN: 67934

Other (OTH) AF: 0.568 AC: 1197 AN: 2106

Alfa AF: 0.559 Hom.: 20952

Bravo AF: 0.596

Asia WGS AF: 0.509 AC: 1767 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.28
PhyloP100		-1.9
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: rs3845823; hg19: chr2-229903121;