1-206629095-C-G

Variant names:

• chr1-206629095-C-G
• rs4845121

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 0.678 in 152,144 control chromosomes in the GnomAD database, including 35,779 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 0.68 (35779 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.678 AC: 103101 AN: 152026 Hom.: 35766 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.678 AC: 103158 AN: 152144 Hom.: 35779 Cov.: 33 AF XY: 0.680 AC XY: 50568 AN XY: 74372

African (AFR) AF: 0.520 AC: 21571 AN: 41488

American (AMR) AF: 0.740 AC: 11322 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3472

East Asian (EAS) AF: 0.781 AC: 4049 AN: 5184

South Asian (SAS) AF: 0.625 AC: 3015 AN: 4826

European-Finnish (FIN) AF: 0.761 AC: 8053 AN: 10576

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49892 AN: 67988

Other (OTH) AF: 0.737 AC: 1559 AN: 2114

Alfa AF: 0.623 Hom.: 2066

Bravo AF: 0.675

Asia WGS AF: 0.668 AC: 2323 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	0.21
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4845121; hg19: chr1-206802440; COSMIC: COSV107160316;