1-111257063-A-G

Variant names:

• chr1-111257063-A-G
• rs17654531

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 0.0832 in 152,230 control chromosomes in the GnomAD database, including 661 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 0.083 (661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0832 AC: 12653 AN: 152112 Hom.: 661 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.00752

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152230 Hom.: 661 Cov.: 32 AF XY: 0.0851 AC XY: 6336 AN XY: 74436

African (AFR) AF: 0.0355 AC: 1474 AN: 41550

American (AMR) AF: 0.0529 AC: 808 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3470

East Asian (EAS) AF: 0.00773 AC: 40 AN: 5174

South Asian (SAS) AF: 0.117 AC: 562 AN: 4818

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7602 AN: 68000

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0965 Hom.: 1523

Bravo AF: 0.0694

Asia WGS AF: 0.0600 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17654531; hg19: chr1-111799685;