rs17259942

Variant names:

• chr12-76678297-A-G
• rs17259942
• ENST00000832799.1:n.643+2053A>G

Variant summary

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

The ENST00000832799.1(ENSG00000257526):​n.643+2053A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,232 control chromosomes in the GnomAD database, including 890 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 0.10 (890 hom., cov: 32)
• Consequence: ENSG00000257526 ENST00000832799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604
• Publications: 5 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832799.1. 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
	ENSG00000257526	ENST00000832799.1		n.643+2053A>G		intron	N/A
	ENSG00000257526	ENST00000832800.1		n.565-39610A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15151 AN: 152114 Hom.: 887 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0995

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0996 AC: 15159 AN: 152232 Hom.: 890 Cov.: 32 AF XY: 0.101 AC XY: 7526 AN XY: 74434

African (AFR) AF: 0.0588 AC: 2443 AN: 41556

American (AMR) AF: 0.118 AC: 1811 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3470

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5184

South Asian (SAS) AF: 0.0584 AC: 282 AN: 4830

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10584

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8290 AN: 68006

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0979 Hom.: 374

Bravo AF: 0.0939

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.26
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs17259942; hg19: chr12-77072077;