1-228064031-G-C

Variant names:

• chr1-228064031-G-C
• rs1745420

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 0.196 in 152,128 control chromosomes in the GnomAD database, including 4,150 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 0.20 (4150 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29743 AN: 152010 Hom.: 4143 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.196 AC: 29790 AN: 152128 Hom.: 4150 Cov.: 33 AF XY: 0.196 AC XY: 14575 AN XY: 74384

African (AFR) AF: 0.391 AC: 16232 AN: 41470

American (AMR) AF: 0.145 AC: 2215 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1229 AN: 5160

South Asian (SAS) AF: 0.159 AC: 765 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1488 AN: 10608

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

European-Non Finnish (NFE) AF: 0.105 AC: 7136 AN: 67988

Other (OTH) AF: 0.155 AC: 328 AN: 2110

Alfa AF: 0.0638 Hom.: 67

Bravo AF: 0.208

Asia WGS AF: 0.199 AC: 690 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	0.033
DANN	Benign	0.41
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1745420; hg19: chr1-228251732;