rs17433222

Variant names:

• chr1-22652153-G-A
• rs17433222
• ENST00000836788.1:n.82-3896C>T

Variant summary

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

The ENST00000836788.1(ENSG00000308848):​n.82-3896C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,102 control chromosomes in the GnomAD database, including 4,436 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 0.23 (4436 hom., cov: 32)
• Consequence: ENSG00000308848 ENST00000836788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 15 publications found

Genes affected

ENSG00000308848 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 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
ENSG00000308848	ENST00000836788.1	n.82-3896C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34863 AN: 151984 Hom.: 4432 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.229 AC: 34871 AN: 152102 Hom.: 4436 Cov.: 32 AF XY: 0.230 AC XY: 17071 AN XY: 74334

African (AFR) AF: 0.126 AC: 5209 AN: 41506

American (AMR) AF: 0.311 AC: 4745 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 626 AN: 3468

East Asian (EAS) AF: 0.143 AC: 736 AN: 5164

South Asian (SAS) AF: 0.180 AC: 866 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2882 AN: 10574

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19097 AN: 67980

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.265 Hom.: 22607

Bravo AF: 0.230

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.71
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs17433222; hg19: chr1-22978646;