rs131794

Variant names:

• chr22-50533323-A-C
• rs131794
• ENST00000739695.1:n.186+2066A>C

Your query was ambiguous. Multiple possible variants found:

• chr22-50533323-A-C
• chr22-50533323-A-G
• chr22-50533323-A-T

Variant summary

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

The ENST00000739695.1(ENSG00000296451):​n.186+2066A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 151,858 control chromosomes in the GnomAD database, including 47,075 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 0.78 (47075 hom., cov: 31)
• Consequence: ENSG00000296451 ENST00000739695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 50 publications found

Genes affected

ENSG00000296451 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296451	ENST00000739695.1	n.186+2066A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119129 AN: 151740 Hom.: 47049 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.785 AC: 119203 AN: 151858 Hom.: 47075 Cov.: 31 AF XY: 0.790 AC XY: 58606 AN XY: 74182

African (AFR) AF: 0.724 AC: 29958 AN: 41358

American (AMR) AF: 0.826 AC: 12607 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4971 AN: 5178

South Asian (SAS) AF: 0.890 AC: 4292 AN: 4820

European-Finnish (FIN) AF: 0.830 AC: 8706 AN: 10486

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53364 AN: 67970

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.794 Hom.: 138401

Bravo AF: 0.784

Asia WGS AF: 0.907 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.33
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs131794; hg19: chr22-50971752;