rs790040

Variant names:

• chr2-232444838-G-A
• rs790040

Your query was ambiguous. Multiple possible variants found:

• chr2-232444838-G-A
• chr2-232444838-G-C

Variant summary

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

The variant allele was found at a frequency of 0.558 in 154,428 control chromosomes in the GnomAD database, including 24,287 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 0.56 (23803 hom., cov: 33)
  • Exomes 𝑓: 0.62 (484 hom.)
• Consequence: DIS3L2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 5 publications found

Genes affected

DIS3L2P1 (HGNC:14021): (DIS3 like 3'-5' exoribonuclease 2 pseudogene 1)

ENSG00000306068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509197.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIS3L2P1	ENST00000509197.1	TSL:6	n.74-29G>A		intron	N/A
	ENSG00000306068	ENST00000815078.1		n.23-482G>A		intron	N/A
	ENSG00000306068	ENST00000815079.1		n.130-482G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84643 AN: 151918 Hom.: 23782 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.622 AC: 1487 AN: 2392 Hom.: 484 Cov.: 0 AF XY: 0.608 AC XY: 801 AN XY: 1318

African (AFR) AF: 0.609 AC: 39 AN: 64

American (AMR) AF: 0.559 AC: 38 AN: 68

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 20 AN: 24

East Asian (EAS) AF: 0.667 AC: 16 AN: 24

South Asian (SAS) AF: 0.712 AC: 302 AN: 424

European-Finnish (FIN) AF: 0.569 AC: 156 AN: 274

Middle Eastern (MID) AF: 0.699 AC: 450 AN: 644

European-Non Finnish (NFE) AF: 0.527 AC: 386 AN: 732

Other (OTH) AF: 0.580 AC: 80 AN: 138

GnomAD4 genome AF: 0.557 AC: 84704 AN: 152036 Hom.: 23803 Cov.: 33 AF XY: 0.559 AC XY: 41517 AN XY: 74310

African (AFR) AF: 0.586 AC: 24312 AN: 41468

American (AMR) AF: 0.558 AC: 8527 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3224 AN: 5154

South Asian (SAS) AF: 0.678 AC: 3266 AN: 4814

European-Finnish (FIN) AF: 0.540 AC: 5716 AN: 10592

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35945 AN: 67938

Other (OTH) AF: 0.567 AC: 1198 AN: 2112

Alfa AF: 0.545 Hom.: 33620

Bravo AF: 0.559

Asia WGS AF: 0.656 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.32
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs790040; hg19: chr2-233309548;