rs2333244

Variant names:

• chr4-175628973-A-T
• rs2333244

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.358 in 151,932 control chromosomes in the GnomAD database, including 10,474 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 0.36 (10474 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.358 AC: 54355 AN: 151812 Hom.: 10461 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.358 AC: 54390 AN: 151932 Hom.: 10474 Cov.: 31 AF XY: 0.364 AC XY: 27046 AN XY: 74238

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.357

Alfa AF: 0.365 Hom.: 1299

Bravo AF: 0.355

Asia WGS AF: 0.428 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2333244; hg19: chr4-176550124;