rs4820571

Variant names:

• chr22-23900786-A-G
• rs4820571
• ENST00000703580.1:n.387-4676T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-23900786-A-G
• chr22-23900786-A-T

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.387-4676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,106 control chromosomes in the GnomAD database, including 26,797 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 0.59 (26797 hom., cov: 33)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 21 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 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.387-4676T>C		intron_variant	Intron 3 of 3
ENSG00000290199	ENST00000717616.1	n.213-9320T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89958 AN: 151988 Hom.: 26774 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.592 AC: 90019 AN: 152106 Hom.: 26797 Cov.: 33 AF XY: 0.599 AC XY: 44507 AN XY: 74344

African (AFR) AF: 0.540 AC: 22396 AN: 41472

American (AMR) AF: 0.597 AC: 9126 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2017 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2619 AN: 5186

South Asian (SAS) AF: 0.687 AC: 3308 AN: 4814

European-Finnish (FIN) AF: 0.648 AC: 6849 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41693 AN: 68006

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.607 Hom.: 21281

Bravo AF: 0.585

Asia WGS AF: 0.613 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4820571; hg19: chr22-24242973; COSMIC: COSV68557436;