rs757219

Variant names:

• chr7-111082426-G-A
• rs757219
• NM_032549.4:c.240-118861C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-111082426-G-A
• chr7-111082426-G-T

Variant summary

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

The NM_032549.4(IMMP2L):​c.240-118861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,120 control chromosomes in the GnomAD database, including 41,490 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 0.70 (41490 hom., cov: 32)
• Consequence: IMMP2L NM_032549.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 6 publications found

Genes affected

IMMP2L (HGNC:14598): (inner mitochondrial membrane peptidase subunit 2) This gene encodes a protein involved in processing the signal peptide sequences used to direct mitochondrial proteins to the mitochondria. The encoded protein resides in the mitochondria and is one of the necessary proteins for the catalytic activity of the mitochondrial inner membrane peptidase (IMP) complex. Two variants that encode the same protein have been described for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMMP2L	NM_032549.4	c.240-118861C>T		intron_variant	Intron 3 of 5	ENST00000405709.7	NP_115938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMMP2L	ENST00000405709.7	c.240-118861C>T		intron_variant	Intron 3 of 5	1	NM_032549.4	ENSP00000384966.2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106875 AN: 152002 Hom.: 41489 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.703 AC: 106890 AN: 152120 Hom.: 41490 Cov.: 32 AF XY: 0.707 AC XY: 52556 AN XY: 74362

African (AFR) AF: 0.341 AC: 14153 AN: 41458

American (AMR) AF: 0.801 AC: 12245 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2436 AN: 3460

East Asian (EAS) AF: 0.809 AC: 4183 AN: 5170

South Asian (SAS) AF: 0.767 AC: 3693 AN: 4818

European-Finnish (FIN) AF: 0.875 AC: 9286 AN: 10610

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58360 AN: 67998

Other (OTH) AF: 0.719 AC: 1519 AN: 2112

Alfa AF: 0.812 Hom.: 81875

Bravo AF: 0.682

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		1.4
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: rs757219; hg19: chr7-110722482;