rs5752809

Variant names:

• chr22-28829512-G-A
• rs5752809
• ENST00000418292.1:n.35-9348G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-28829512-G-A
• chr22-28829512-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418292.1(ENSG00000226471):​n.35-9348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,764 control chromosomes in the GnomAD database, including 13,304 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 0.40 (13304 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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
ENSG00000226471	ENST00000418292.1	n.35-9348G>A		intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000458080.1	n.263+7333G>A		intron_variant	Intron 2 of 3	3
ENSG00000226471	ENST00000687270.1	n.258+7333G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60355 AN: 151648 Hom.: 13279 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.398 AC: 60435 AN: 151764 Hom.: 13304 Cov.: 31 AF XY: 0.401 AC XY: 29757 AN XY: 74142

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.377

Alfa AF: 0.363 Hom.: 1343

Bravo AF: 0.398

Asia WGS AF: 0.609 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5752809; hg19: chr22-29225500;