22-19748305-G-C

Variant names:

• chr22-19748305-G-C
• rs8135854
• ENST00000816392.1:n.*217C>G

Variant summary

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

The ENST00000816392.1(ENSG00000306238):​n.*217C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,972 control chromosomes in the GnomAD database, including 11,493 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 (11493 hom., cov: 32)
• Consequence: ENSG00000306238 ENST00000816392.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 1 publications found

Genes affected

ENSG00000306238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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
ENSG00000306238	ENST00000816392.1	n.*217C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57526 AN: 151854 Hom.: 11478 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.379 AC: 57597 AN: 151972 Hom.: 11493 Cov.: 32 AF XY: 0.375 AC XY: 27846 AN XY: 74240

African (AFR) AF: 0.298 AC: 12355 AN: 41440

American (AMR) AF: 0.413 AC: 6314 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.119 AC: 616 AN: 5170

South Asian (SAS) AF: 0.431 AC: 2070 AN: 4808

European-Finnish (FIN) AF: 0.371 AC: 3909 AN: 10546

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29863 AN: 67950

Other (OTH) AF: 0.380 AC: 801 AN: 2110

Alfa AF: 0.261 Hom.: 631

Bravo AF: 0.378

Asia WGS AF: 0.285 AC: 988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.76
DANN	Benign	0.43
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs8135854; hg19: chr22-19735828;