chr1-30587551-C-T

Variant names:

• chr1-30587551-C-T
• rs471202

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 0.243 in 151,862 control chromosomes in the GnomAD database, including 4,894 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 0.24 (4894 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.243 AC: 36896 AN: 151746 Hom.: 4875 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.0963

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.243 AC: 36949 AN: 151862 Hom.: 4894 Cov.: 31 AF XY: 0.242 AC XY: 17962 AN XY: 74206

African (AFR) AF: 0.347 AC: 14346 AN: 41366

American (AMR) AF: 0.171 AC: 2616 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1525 AN: 5142

South Asian (SAS) AF: 0.0968 AC: 465 AN: 4804

European-Finnish (FIN) AF: 0.265 AC: 2794 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13644 AN: 67930

Other (OTH) AF: 0.205 AC: 433 AN: 2114

Alfa AF: 0.204 Hom.: 1872

Bravo AF: 0.244

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs471202; hg19: chr1-31060398; COSMIC: COSV59935857;