rs2577720

Variant names:

• chr2-23325743-A-C
• rs2577720

Your query was ambiguous. Multiple possible variants found:

• chr2-23325743-A-C
• chr2-23325743-A-G
• chr2-23325743-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.471

Alfa AF: 0.514 Hom.: 31128

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577720; hg19: chr2-23548614;