rs6436839

Variant names:

• chr2-229105082-A-G
• rs6436839
• NM_001100818.2:c.177+50736T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-229105082-A-G
• chr2-229105082-A-T

Variant summary

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

The NM_001100818.2(PID1):​c.177+50736T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,170 control chromosomes in the GnomAD database, including 6,939 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 (6939 hom., cov: 33)
• Consequence: PID1 NM_001100818.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 10 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001100818.2. 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.177+50736T>C		intron	N/A	NP_001094288.1
	PID1	NM_001330156.1		c.276+50736T>C		intron	N/A	NP_001317085.1
	PID1	NM_017933.5		c.270+50736T>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.177+50736T>C		intron	N/A	ENSP00000375908.3
	PID1	ENST00000409462.1	TSL:1	c.31-78974T>C		intron	N/A	ENSP00000386826.1
	PID1	ENST00000354069.6	TSL:3	c.276+50736T>C		intron	N/A	ENSP00000283937.8

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45370 AN: 152052 Hom.: 6944 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.298 AC: 45386 AN: 152170 Hom.: 6939 Cov.: 33 AF XY: 0.301 AC XY: 22409 AN XY: 74398

African (AFR) AF: 0.355 AC: 14739 AN: 41512

American (AMR) AF: 0.328 AC: 5011 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5164

South Asian (SAS) AF: 0.342 AC: 1654 AN: 4830

European-Finnish (FIN) AF: 0.278 AC: 2947 AN: 10584

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17601 AN: 67996

Other (OTH) AF: 0.293 AC: 619 AN: 2112

Alfa AF: 0.272 Hom.: 19773

Bravo AF: 0.302

Asia WGS AF: 0.326 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.34
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: rs6436839; hg19: chr2-229969798;