1-204154543-G-C

Variant names:

• chr1-204154543-G-C
• rs11571093

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 0.0617 in 152,236 control chromosomes in the GnomAD database, including 337 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 0.062 (337 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579
• Publications: 8 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 = 0.107 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: 0.0618 AC: 9395 AN: 152118 Hom.: 338 Cov.: 33

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0617 AC: 9390 AN: 152236 Hom.: 337 Cov.: 33 AF XY: 0.0622 AC XY: 4627 AN XY: 74430

African (AFR) AF: 0.0235 AC: 978 AN: 41544

American (AMR) AF: 0.0524 AC: 801 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3470

East Asian (EAS) AF: 0.112 AC: 580 AN: 5174

South Asian (SAS) AF: 0.115 AC: 552 AN: 4818

European-Finnish (FIN) AF: 0.0682 AC: 723 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5131 AN: 68022

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0650 Hom.: 43

Bravo AF: 0.0568

Asia WGS AF: 0.0940 AC: 325 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	3.7
DANN	Benign	0.39
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs11571093; hg19: chr1-204123671;