22-28760460-A-G

Variant names:

• chr22-28760460-A-G
• rs6005863
• ENST00000729538.1:n.204+145A>G

Variant summary

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

The ENST00000729538.1(ENSG00000295361):​n.204+145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,858 control chromosomes in the GnomAD database, including 17,918 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 0.48 (17918 hom., cov: 31)
• Consequence: ENSG00000295361 ENST00000729538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 17 publications found

Genes affected

ENSG00000295361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729538.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295361	ENST00000729538.1		n.204+145A>G		intron	N/A
	ENSG00000295361	ENST00000729539.1		n.205+145A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72164 AN: 151738 Hom.: 17881 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.476 AC: 72250 AN: 151858 Hom.: 17918 Cov.: 31 AF XY: 0.484 AC XY: 35892 AN XY: 74206

African (AFR) AF: 0.509 AC: 21034 AN: 41364

American (AMR) AF: 0.465 AC: 7087 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2104 AN: 3468

East Asian (EAS) AF: 0.783 AC: 4056 AN: 5178

South Asian (SAS) AF: 0.713 AC: 3436 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5013 AN: 10534

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28006 AN: 67940

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

Alfa AF: 0.441 Hom.: 63630

Bravo AF: 0.477

Asia WGS AF: 0.758 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6005863; hg19: chr22-29156448;