rs782603

chr2-55623128-A-Gchr2-55623128-A-T

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 0.933 in 152,250 control chromosomes in the GnomAD database, including 66,835 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 0.93 (66835 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141932 AN: 152132 Hom.: 66793 Cov.: 31

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.933 AC: 142027 AN: 152250 Hom.: 66835 Cov.: 31 AF XY: 0.929 AC XY: 69147 AN XY: 74432

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.911

Alfa AF: 0.946 Hom.: 8476

Bravo AF: 0.932

Asia WGS AF: 0.682 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782603; hg19: chr2-55850263;