rs2760051

chr1-188151222-A-Gchr1-188151222-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 0.542 in 151,580 control chromosomes in the GnomAD database, including 22,311 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 0.54 (22311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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: 0.541 AC: 82016 AN: 151462 Hom.: 22280 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.542 AC: 82086 AN: 151580 Hom.: 22311 Cov.: 32 AF XY: 0.543 AC XY: 40245 AN XY: 74110

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.538

Alfa AF: 0.514 Hom.: 8317

Bravo AF: 0.540

Asia WGS AF: 0.627 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.0
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: rs2760051; hg19: chr1-188120353;