rs8559

Variant names:

• chr1-28237741-A-C
• rs8559
• ENST00000465645.1:c.*1285A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-28237741-A-C
• chr1-28237741-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_178191.3(ATP5IF1):​c.*1285A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ATP5IF1 NM_178191.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

ATP5IF1 (HGNC:871): (ATP synthase inhibitory factor subunit 1) Enables several functions, including ATPase binding activity; angiostatin binding activity; and mitochondrial proton-transporting ATP synthase complex binding activity. Involved in several processes, including mitochondrial depolarization; negative regulation of ATPase activity; and regulation of protein targeting to mitochondrion. Located in cell surface and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP5IF1	NM_016311.5	c.180-96A>C		intron_variant	Intron 2 of 2	ENST00000335514.10	NP_057395.1
ATP5IF1	NM_178191.3	c.*1285A>C		3_prime_UTR_variant	Exon 2 of 2		NP_835498.1
ATP5IF1	NM_178190.3	c.180-20A>C		intron_variant	Intron 2 of 2		NP_835497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP5IF1	ENST00000465645.1	c.*1285A>C		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000437337.1
ATP5IF1	ENST00000335514.10	c.180-96A>C		intron_variant	Intron 2 of 2	1	NM_016311.5	ENSP00000335203.5
ATP5IF1	ENST00000468425.2	c.179+1289A>C		intron_variant	Intron 2 of 2	2		ENSP00000435341.1
ATP5IF1	ENST00000497986.5	c.180-20A>C		intron_variant	Intron 2 of 2	2		ENSP00000435579.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs8559; hg19: chr1-28564252;