rs1046099

Positions:

• chr14-93183156-A-G
• chr14-93183156-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022151.5(MOAP1):​c.*31T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 1,564,022 control chromosomes in the GnomAD database, including 366,217 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 0.69 (36609 hom., cov: 32)
  • Exomes 𝑓: 0.68 (329608 hom.)
• Consequence: MOAP1 NM_022151.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

MOAP1 (HGNC:16658): (modulator of apoptosis 1) The protein encoded by this gene was identified by its interaction with apoptosis regulator BAX protein. This protein contains a Bcl-2 homology 3 (BH3)-like motif, which is required for the association with BAX. When overexpressed, this gene has been shown to mediate caspase-dependent apoptosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOAP1	NM_022151.5	c.*31T>C		3_prime_UTR_variant	3/3	ENST00000298894.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOAP1	ENST00000298894.5	c.*31T>C		3_prime_UTR_variant	3/3	1	NM_022151.5	P1
MOAP1	ENST00000556883.1	c.*31T>C		3_prime_UTR_variant	2/2	2		P1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105133 AN: 151950 Hom.: 36582 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.708

GnomAD3 exomes AF: 0.678 AC: 143615 AN: 211968 Hom.: 48763 AF XY: 0.680 AC XY: 77071 AN XY: 113300

Gnomad AFR exome AF: 0.752

Gnomad AMR exome AF: 0.628

Gnomad ASJ exome AF: 0.608

Gnomad EAS exome AF: 0.697

Gnomad SAS exome AF: 0.726

Gnomad FIN exome AF: 0.667

Gnomad NFE exome AF: 0.672

Gnomad OTH exome AF: 0.682

GnomAD4 exome AF: 0.683 AC: 963681 AN: 1411954 Hom.: 329608 Cov.: 53 AF XY: 0.683 AC XY: 476725 AN XY: 697828

Gnomad4 AFR exome AF: 0.757

Gnomad4 AMR exome AF: 0.637

Gnomad4 ASJ exome AF: 0.606

Gnomad4 EAS exome AF: 0.713

Gnomad4 SAS exome AF: 0.726

Gnomad4 FIN exome AF: 0.668

Gnomad4 NFE exome AF: 0.680

Gnomad4 OTH exome AF: 0.686

GnomAD4 genome AF: 0.692 AC: 105216 AN: 152068 Hom.: 36609 Cov.: 32 AF XY: 0.688 AC XY: 51146 AN XY: 74336

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.708

Alfa AF: 0.673 Hom.: 47879

Bravo AF: 0.696

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.74

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: rs1046099; hg19: chr14-93649501;