ENST00000810418.1:n.347+772T>G

Variant names:

• chr22-28849243-T-G
• rs5762853
• ENST00000810418.1:n.347+772T>G

Variant summary

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

The ENST00000810418.1(ENSG00000226471):​n.347+772T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,740 control chromosomes in the GnomAD database, including 8,117 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 0.31 (8117 hom., cov: 29)
• Consequence: ENSG00000226471 ENST00000810418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 9 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810418.1. 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
	ENSG00000226471	ENST00000810418.1		n.347+772T>G		intron	N/A
	ENSG00000226471	ENST00000810419.1		n.266-1004T>G		intron	N/A
	ENSG00000226471	ENST00000810420.1		n.611+772T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46813 AN: 151622 Hom.: 8104 Cov.: 29

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.309 AC: 46875 AN: 151740 Hom.: 8117 Cov.: 29 AF XY: 0.313 AC XY: 23202 AN XY: 74144

African (AFR) AF: 0.385 AC: 15914 AN: 41372

American (AMR) AF: 0.257 AC: 3910 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1084 AN: 3466

East Asian (EAS) AF: 0.674 AC: 3458 AN: 5128

South Asian (SAS) AF: 0.498 AC: 2390 AN: 4796

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10546

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16278 AN: 67898

Other (OTH) AF: 0.318 AC: 670 AN: 2108

Alfa AF: 0.293 Hom.: 2483

Bravo AF: 0.309

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs5762853; hg19: chr22-29245231;