22-40685223-G-T

Variant names:

• chr22-40685223-G-T
• rs882111
• ENST00000842895.1:n.145+49G>T

Variant summary

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

The ENST00000842895.1(ENSG00000309667):​n.145+49G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 152,234 control chromosomes in the GnomAD database, including 271 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 0.052 (271 hom., cov: 31)
• Consequence: ENSG00000309667 ENST00000842895.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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+49G>T		intron_variant	Intron 1 of 1
ENSG00000309667	ENST00000842896.1	n.162+49G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7872 AN: 152116 Hom.: 271 Cov.: 31

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0466

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

GnomAD4 genome AF: 0.0517 AC: 7874 AN: 152234 Hom.: 271 Cov.: 31 AF XY: 0.0514 AC XY: 3822 AN XY: 74422

African (AFR) AF: 0.0179 AC: 742 AN: 41544

American (AMR) AF: 0.0656 AC: 1003 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0472 AC: 164 AN: 3472

East Asian (EAS) AF: 0.0838 AC: 434 AN: 5176

South Asian (SAS) AF: 0.134 AC: 644 AN: 4812

European-Finnish (FIN) AF: 0.0219 AC: 233 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4536 AN: 68014

Other (OTH) AF: 0.0466 AC: 98 AN: 2104

Alfa AF: 0.0589 Hom.: 387

Bravo AF: 0.0504

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs882111; hg19: chr22-41081227;