rs300723

Variant names:

• chr2-134131-C-T
• rs300723

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 0.792 in 152,090 control chromosomes in the GnomAD database, including 47,870 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 0.79 (47870 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.792 AC: 120321 AN: 151972 Hom.: 47838 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.792 AC: 120396 AN: 152090 Hom.: 47870 Cov.: 32 AF XY: 0.792 AC XY: 58898 AN XY: 74350

African (AFR) AF: 0.769 AC: 31890 AN: 41460

American (AMR) AF: 0.710 AC: 10864 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2808 AN: 3468

East Asian (EAS) AF: 0.891 AC: 4601 AN: 5164

South Asian (SAS) AF: 0.678 AC: 3265 AN: 4814

European-Finnish (FIN) AF: 0.869 AC: 9208 AN: 10594

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55123 AN: 67974

Other (OTH) AF: 0.768 AC: 1625 AN: 2116

Alfa AF: 0.799 Hom.: 6972

Bravo AF: 0.778

Asia WGS AF: 0.738 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.20
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs300723; hg19: chr2-134131;