22-47359575-G-T

Variant names:

• chr22-47359575-G-T
• rs11090762
• ENST00000434707.1:n.157-4017G>T

Variant summary

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

The ENST00000434707.1(ENSG00000224715):​n.157-4017G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,080 control chromosomes in the GnomAD database, including 17,307 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 0.46 (17307 hom., cov: 33)
• Consequence: ENSG00000224715 ENST00000434707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 4 publications found

Genes affected

ENSG00000224715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339685	NR_144462.2	n.155-4017G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224715	ENST00000434707.1	n.157-4017G>T		intron_variant	Intron 1 of 3	1
ENSG00000224715	ENST00000758540.1	n.101-7193G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69767 AN: 151962 Hom.: 17284 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.459 AC: 69819 AN: 152080 Hom.: 17307 Cov.: 33 AF XY: 0.464 AC XY: 34483 AN XY: 74340

African (AFR) AF: 0.276 AC: 11440 AN: 41458

American (AMR) AF: 0.572 AC: 8741 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1781 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1585 AN: 5172

South Asian (SAS) AF: 0.594 AC: 2862 AN: 4822

European-Finnish (FIN) AF: 0.552 AC: 5834 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35797 AN: 67980

Other (OTH) AF: 0.468 AC: 990 AN: 2114

Alfa AF: 0.492 Hom.: 25036

Bravo AF: 0.450

Asia WGS AF: 0.492 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.48
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs11090762; hg19: chr22-47755325;