rs905568

Variant names:

• chr3-114232449-C-A
• rs905568
• ENST00000473625.1:n.573G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-114232449-C-A
• chr3-114232449-C-G
• chr3-114232449-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000473625.1(ATOSBP1):​n.573G>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 0.0000605 in 479,720 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000059 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000061 (0 hom.)
• Consequence: ATOSBP1 ENST00000473625.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 11 publications found

Genes affected

ATOSBP1 (HGNC:54597): (ATOSB pseudogene 1)

ENSG00000241490 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473625.1. 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
	ATOSBP1	ENST00000473625.1	TSL:6	n.573G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000241490	ENST00000481773.2	TSL:3	n.239-893C>A		intron	N/A
	ENSG00000241490	ENST00000493033.1	TSL:2	n.161-893C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000592 AC: 9 AN: 151968 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000966

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000736

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000610 AC: 20 AN: 327752 Hom.: 0 Cov.: 0 AF XY: 0.0000681 AC XY: 12 AN XY: 176120

African (AFR) AF: 0.00 AC: 0 AN: 7646

American (AMR) AF: 0.00 AC: 0 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8924

East Asian (EAS) AF: 0.00 AC: 0 AN: 16388

South Asian (SAS) AF: 0.0000897 AC: 3 AN: 33434

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28236

Middle Eastern (MID) AF: 0.00274 AC: 8 AN: 2924

European-Non Finnish (NFE) AF: 0.0000356 AC: 7 AN: 196632

Other (OTH) AF: 0.000109 AC: 2 AN: 18412

GnomAD4 genome AF: 0.0000592 AC: 9 AN: 151968 Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3 AN XY: 74222

African (AFR) AF: 0.0000966 AC: 4 AN: 41390

American (AMR) AF: 0.00 AC: 0 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.00 AC: 0 AN: 4836

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000736 AC: 5 AN: 67932

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 980

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs905568; hg19: chr3-113951296;