rs466755

Variant names:

• chr22-18048218-A-G
• rs466755
• ENST00000801416.1:n.97+3939A>G

Variant summary

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

The ENST00000801416.1(ENSG00000304254):​n.97+3939A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,008 control chromosomes in the GnomAD database, including 663 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 0.077 (663 hom., cov: 32)
• Consequence: ENSG00000304254 ENST00000801416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 5 publications found

Genes affected

ENSG00000304254 (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 (SAS) allele frequency at 95% confidence interval = 0.244 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
ENSG00000304254	ENST00000801416.1	n.97+3939A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11650 AN: 151890 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0767 AC: 11656 AN: 152008 Hom.: 663 Cov.: 32 AF XY: 0.0825 AC XY: 6132 AN XY: 74302

African (AFR) AF: 0.0480 AC: 1991 AN: 41474

American (AMR) AF: 0.142 AC: 2164 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1278 AN: 5162

South Asian (SAS) AF: 0.256 AC: 1226 AN: 4798

European-Finnish (FIN) AF: 0.0610 AC: 644 AN: 10566

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3887 AN: 67958

Other (OTH) AF: 0.0692 AC: 146 AN: 2110

Alfa AF: 0.0681 Hom.: 997

Bravo AF: 0.0795

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.18
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs466755; hg19: chr22-18530984;