rs2723333

Variant names:

• chr4-110777935-G-A
• rs2723333

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 0.0728 in 152,202 control chromosomes in the GnomAD database, including 499 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 0.073 (499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991
• Publications: 3 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0728 AC: 11070 AN: 152084 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0728 AC: 11073 AN: 152202 Hom.: 499 Cov.: 32 AF XY: 0.0720 AC XY: 5358 AN XY: 74412

African (AFR) AF: 0.0180 AC: 749 AN: 41544

American (AMR) AF: 0.0726 AC: 1110 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1172 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6994 AN: 67992

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0784 Hom.: 226

Bravo AF: 0.0664

Asia WGS AF: 0.0400 AC: 140 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	6.5
DANN	Benign	0.47
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs2723333; hg19: chr4-111699091;