ENST00000842895.1:n.145+4791A>G

Variant names:

• chr22-40689965-A-G
• rs80533
• ENST00000842895.1:n.145+4791A>G

Variant summary

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

The ENST00000842895.1(ENSG00000309667):​n.145+4791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,096 control chromosomes in the GnomAD database, including 51,003 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 0.81 (51003 hom., cov: 31)
• Consequence: ENSG00000309667 ENST00000842895.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 13 publications found

Genes affected

ENSG00000309667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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
ENSG00000309667	ENST00000842895.1	n.145+4791A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123220 AN: 151978 Hom.: 50946 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.811 AC: 123323 AN: 152096 Hom.: 51003 Cov.: 31 AF XY: 0.805 AC XY: 59888 AN XY: 74362

African (AFR) AF: 0.949 AC: 39405 AN: 41520

American (AMR) AF: 0.597 AC: 9108 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2792 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4969 AN: 5180

South Asian (SAS) AF: 0.787 AC: 3788 AN: 4816

European-Finnish (FIN) AF: 0.783 AC: 8274 AN: 10568

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52568 AN: 67978

Other (OTH) AF: 0.799 AC: 1681 AN: 2104

Alfa AF: 0.786 Hom.: 31446

Bravo AF: 0.798

Asia WGS AF: 0.874 AC: 3039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs80533; hg19: chr22-41085969;