1-188151222-A-G

Variant names:

• chr1-188151222-A-G
• rs2760051

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 0.542 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.527 AC: 21817 AN: 41412

American (AMR) AF: 0.565 AC: 8595 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.650 AC: 3353 AN: 5160

South Asian (SAS) AF: 0.603 AC: 2902 AN: 4816

European-Finnish (FIN) AF: 0.562 AC: 5930 AN: 10548

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36143 AN: 67652

Other (OTH) AF: 0.538 AC: 1133 AN: 2104

Alfa AF: 0.515 Hom.: 9467

Bravo AF: 0.540

Asia WGS AF: 0.627 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.81
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs2760051; hg19: chr1-188120353;