14-53991360-C-T

Variant names:

• chr14-53991360-C-T
• rs1957844
• ENST00000441945.2:n.636G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000441945.2(ATP5F1CP1):​n.636G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 1,023,816 control chromosomes in the GnomAD database, including 262,454 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 0.65 (33992 hom., cov: 31)
  • Exomes 𝑓: 0.72 (228462 hom.)
• Consequence: ATP5F1CP1 ENST00000441945.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25
• Publications: 11 publications found

Genes affected

ATP5F1CP1 (HGNC:834): (ATP synthase F1 subunit gamma pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP5F1CP1		n.53991360C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP5F1CP1	ENST00000441945.2	n.636G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98536 AN: 151886 Hom.: 33995 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.679

GnomAD4 exome AF: 0.718 AC: 626145 AN: 871812 Hom.: 228462 Cov.: 12 AF XY: 0.721 AC XY: 329607 AN XY: 457190

African (AFR) AF: 0.388 AC: 8972 AN: 23100

American (AMR) AF: 0.605 AC: 26128 AN: 43208

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 15480 AN: 22254

East Asian (EAS) AF: 0.484 AC: 17990 AN: 37150

South Asian (SAS) AF: 0.684 AC: 50765 AN: 74194

European-Finnish (FIN) AF: 0.729 AC: 38038 AN: 52164

Middle Eastern (MID) AF: 0.726 AC: 3220 AN: 4438

European-Non Finnish (NFE) AF: 0.761 AC: 436920 AN: 574394

Other (OTH) AF: 0.700 AC: 28632 AN: 40910

GnomAD4 genome AF: 0.648 AC: 98560 AN: 152004 Hom.: 33992 Cov.: 31 AF XY: 0.647 AC XY: 48046 AN XY: 74310

African (AFR) AF: 0.408 AC: 16907 AN: 41404

American (AMR) AF: 0.673 AC: 10273 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2372 AN: 5166

South Asian (SAS) AF: 0.661 AC: 3184 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7814 AN: 10560

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53277 AN: 68000

Other (OTH) AF: 0.679 AC: 1432 AN: 2110

Alfa AF: 0.737 Hom.: 176993

Bravo AF: 0.629

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	8.6
DANN	Benign	0.78
PhyloP100		3.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1957844; hg19: chr14-54458078;