chr2-23325743-A-C

Variant names:

• chr2-23325743-A-C
• rs2577720

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.476 in 152,070 control chromosomes in the GnomAD database, including 17,711 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 0.48 (17711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 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: 0.477 AC: 72450 AN: 151952 Hom.: 17716 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.476 AC: 72440 AN: 152070 Hom.: 17711 Cov.: 32 AF XY: 0.479 AC XY: 35586 AN XY: 74326

African (AFR) AF: 0.368 AC: 15259 AN: 41478

American (AMR) AF: 0.485 AC: 7417 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1972 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2922 AN: 4808

European-Finnish (FIN) AF: 0.564 AC: 5966 AN: 10584

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35451 AN: 67954

Other (OTH) AF: 0.471 AC: 995 AN: 2112

Alfa AF: 0.506 Hom.: 69154

Bravo AF: 0.459

Asia WGS AF: 0.496 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2577720; hg19: chr2-23548614;