22-23924860-C-T

Variant names:

• chr22-23924860-C-T
• rs5751777
• ENST00000703580.1:n.386+1584G>A

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.386+1584G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 150,902 control chromosomes in the GnomAD database, including 24,221 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 0.56 (24221 hom., cov: 29)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 30 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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
ENSG00000290199	ENST00000703580.1	n.386+1584G>A		intron_variant	Intron 3 of 3
ENSG00000290199	ENST00000717616.1	n.212+1584G>A		intron_variant	Intron 2 of 2
ENSG00000290199	ENST00000717617.1	n.213-131G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85217 AN: 150796 Hom.: 24205 Cov.: 29

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.565 AC: 85258 AN: 150902 Hom.: 24221 Cov.: 29 AF XY: 0.571 AC XY: 42029 AN XY: 73560

African (AFR) AF: 0.497 AC: 20384 AN: 41026

American (AMR) AF: 0.575 AC: 8730 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.490 AC: 2519 AN: 5144

South Asian (SAS) AF: 0.699 AC: 3346 AN: 4788

European-Finnish (FIN) AF: 0.629 AC: 6377 AN: 10146

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 39973 AN: 67842

Other (OTH) AF: 0.559 AC: 1174 AN: 2100

Alfa AF: 0.571 Hom.: 8202

Bravo AF: 0.554

Asia WGS AF: 0.597 AC: 2075 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5751777; hg19: chr22-24267047;