chr1-55037775-A-G

Variant names:

• chr1-55037775-A-G
• rs17111503

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 0.233 in 152,078 control chromosomes in the GnomAD database, including 5,260 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 0.23 (5260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.233 AC: 35380 AN: 151958 Hom.: 5257 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.233 AC: 35397 AN: 152078 Hom.: 5260 Cov.: 32 AF XY: 0.233 AC XY: 17299 AN XY: 74334

African (AFR) AF: 0.0968 AC: 4020 AN: 41528

American (AMR) AF: 0.324 AC: 4945 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1014 AN: 3466

East Asian (EAS) AF: 0.679 AC: 3491 AN: 5140

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18062 AN: 67952

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.256 Hom.: 3043

Bravo AF: 0.241

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs17111503; hg19: chr1-55503448;