22-28803802-G-T

Variant names:

• chr22-28803802-G-T
• rs6005893
• ENST00000418292.1:n.34+3065G>T

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.34+3065G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,920 control chromosomes in the GnomAD database, including 1,497 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 0.11 (1497 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418292.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226471	ENST00000418292.1	TSL:3	n.34+3065G>T		intron	N/A
	ENSG00000226471	ENST00000451486.5	TSL:5	n.103+1808G>T		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.55+3065G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17423 AN: 151802 Hom.: 1491 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.115 AC: 17470 AN: 151920 Hom.: 1497 Cov.: 31 AF XY: 0.114 AC XY: 8485 AN XY: 74260

African (AFR) AF: 0.227 AC: 9383 AN: 41366

American (AMR) AF: 0.104 AC: 1580 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0707 AC: 245 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1431 AN: 5174

South Asian (SAS) AF: 0.0648 AC: 312 AN: 4812

European-Finnish (FIN) AF: 0.0630 AC: 664 AN: 10538

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0526 AC: 3576 AN: 67982

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0690 Hom.: 1070

Bravo AF: 0.125

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.5
DANN	Benign	0.84
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6005893; hg19: chr22-29199790;