rs5752809

Positions:

• 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 ENST00000458080.1(ENSG00000226471):​n.263+7333G>A variant causes a intron, non coding transcript 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: ENST00000458080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000458080.1	n.263+7333G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000418292.1	n.35-9348G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000687270.1	n.258+7333G>A		intron_variant, non_coding_transcript_variant

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;