rs5762839

chr22-28835459-C-T

Variant summary

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

The ENST00000458080.1(ENSG00000226471):n.264-8668C>T 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 0.147 in 152,188 control chromosomes in the GnomAD database, including 1,988 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 0.15 (1988 hom., cov: 32)
• Consequence: ENST00000458080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 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.264-8668C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000418292.1	n.35-3401C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000687270.1	n.259-8668C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22329 AN: 152070 Hom.: 1988 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.147 AC: 22338 AN: 152188 Hom.: 1988 Cov.: 32 AF XY: 0.152 AC XY: 11322 AN XY: 74402

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.176

Alfa AF: 0.171 Hom.: 1306

Bravo AF: 0.135

Asia WGS AF: 0.340 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5762839; hg19: chr22-29231447;