rs1709920

Variant names:

• chr3-106897997-G-A
• rs1709920
• ENST00000484698.5:n.628+22969C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-106897997-G-A
• chr3-106897997-G-C
• chr3-106897997-G-T

Variant summary

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

The ENST00000507369.1(MTATP6P22):​n.272C>T 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 0.815 in 152,124 control chromosomes in the GnomAD database, including 50,808 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 0.82 (50805 hom., cov: 31)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: MTATP6P22 ENST00000507369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 1 publications found

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

MTATP6P22 (HGNC:52178): (MT-ATP6 pseudogene 22)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507369.1. 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
	LINC00882	ENST00000484698.5	TSL:1	n.628+22969C>T		intron	N/A
	MTATP6P22	ENST00000507369.1	TSL:6	n.272C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC00882	ENST00000655451.1		n.729+15045C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123955 AN: 151998 Hom.: 50805 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.817

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.815 AC: 123989 AN: 152116 Hom.: 50805 Cov.: 31 AF XY: 0.819 AC XY: 60860 AN XY: 74354

African (AFR) AF: 0.741 AC: 30706 AN: 41442

American (AMR) AF: 0.782 AC: 11946 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3468

East Asian (EAS) AF: 0.849 AC: 4395 AN: 5174

South Asian (SAS) AF: 0.926 AC: 4469 AN: 4828

European-Finnish (FIN) AF: 0.915 AC: 9703 AN: 10608

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 57017 AN: 68014

Other (OTH) AF: 0.819 AC: 1729 AN: 2112

Alfa AF: 0.830 Hom.: 10939

Bravo AF: 0.800

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.17
DANN	Benign	0.35
PhyloP100		0.90

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: rs1709920;

hg19: chr3-106616844;