chr22-48210499-A-G

Variant names:

• chr22-48210499-A-G
• rs9306510
• ENST00000818596.1:n.-166T>C

Variant summary

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

The ENST00000818596.1(ENSG00000306452):​n.-166T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,116 control chromosomes in the GnomAD database, including 11,005 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 0.38 (11005 hom., cov: 33)
• Consequence: ENSG00000306452 ENST00000818596.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 5 publications found

Genes affected

ENSG00000306452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818596.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306452	ENST00000818596.1		n.-166T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57014 AN: 152000 Hom.: 10971 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 57092 AN: 152116 Hom.: 11005 Cov.: 33 AF XY: 0.373 AC XY: 27718 AN XY: 74356

African (AFR) AF: 0.449 AC: 18643 AN: 41480

American (AMR) AF: 0.433 AC: 6624 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2119 AN: 5156

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3113 AN: 10580

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22435 AN: 67998

Other (OTH) AF: 0.378 AC: 799 AN: 2116

Alfa AF: 0.353 Hom.: 31493

Bravo AF: 0.390

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.26
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9306510; hg19: chr22-48606311;