rs972153

Variant names:

• chr22-35704363-C-A
• rs972153
• ENST00000415961.2:n.*187C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-35704363-C-A
• chr22-35704363-C-T

Variant summary

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

The ENST00000415961.2(MRPS16P3):​n.*187C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 151,980 control chromosomes in the GnomAD database, including 36,659 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 (36659 hom., cov: 31)
• Consequence: MRPS16P3 ENST00000415961.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

Genes affected

MRPS16P3 (HGNC:29733): (mitochondrial ribosomal protein S16 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS16P3	ENST00000415961.2	n.*187C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104477 AN: 151862 Hom.: 36627 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.688 AC: 104566 AN: 151980 Hom.: 36659 Cov.: 31 AF XY: 0.684 AC XY: 50823 AN XY: 74284

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.684

Alfa AF: 0.599 Hom.: 3596

Bravo AF: 0.693

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972153; hg19: chr22-36100410;