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 ENST00000484698.5(LINC00882):​n.628+22969C>T variant causes a intron 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: LINC00882 ENST00000484698.5 intron
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTATP6P22		n.106897997G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00882	ENST00000484698.5	n.628+22969C>T		intron_variant	Intron 6 of 7	1
MTATP6P22	ENST00000507369.1	n.272C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC00882	ENST00000655451.1	n.729+15045C>T		intron_variant	Intron 7 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs1709920; hg19: chr3-106616844;