16-10724951-C-G

Variant names:

• chr16-10724951-C-G
• rs12924823
• ENST00000576835.1:n.346G>C

Variant summary

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

The ENST00000576835.1(MTATP6P24):​n.346G>C 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 0.137 in 152,096 control chromosomes in the GnomAD database, including 1,554 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 0.14 (1554 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTATP6P24 ENST00000576835.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 2 publications found

Genes affected

MTATP6P24 (HGNC:52180): (MT-ATP6 pseudogene 24)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576835.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTATP6P24	ENST00000576835.1	TSL:6	n.346G>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20857 AN: 151976 Hom.: 1551 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.0999

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.137 AC: 20884 AN: 152096 Hom.: 1554 Cov.: 32 AF XY: 0.136 AC XY: 10110 AN XY: 74340

African (AFR) AF: 0.168 AC: 6979 AN: 41464

American (AMR) AF: 0.0804 AC: 1229 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3468

East Asian (EAS) AF: 0.0501 AC: 260 AN: 5186

South Asian (SAS) AF: 0.203 AC: 974 AN: 4808

European-Finnish (FIN) AF: 0.129 AC: 1364 AN: 10574

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9425 AN: 67994

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.0445 Hom.: 45

Bravo AF: 0.129

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12924823;

hg19: chr16-10818808;