rs4233285

Variant names:

• chr1-22349799-T-C
• rs4233285

Variant summary

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

The variant allele was found at a frequency of 0.647 in 152,054 control chromosomes in the GnomAD database, including 31,948 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 0.65 (31948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 5 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.72 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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98225 AN: 151936 Hom.: 31901 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.647 AC: 98328 AN: 152054 Hom.: 31948 Cov.: 33 AF XY: 0.647 AC XY: 48110 AN XY: 74330

African (AFR) AF: 0.711 AC: 29502 AN: 41494

American (AMR) AF: 0.611 AC: 9340 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3815 AN: 5158

South Asian (SAS) AF: 0.671 AC: 3236 AN: 4824

European-Finnish (FIN) AF: 0.628 AC: 6637 AN: 10568

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41826 AN: 67938

Other (OTH) AF: 0.605 AC: 1278 AN: 2114

Alfa AF: 0.636 Hom.: 3823

Bravo AF: 0.647

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4233285; hg19: chr1-22676292;