1-154696818-G-A

Variant names:

• chr1-154696818-G-A
• rs2172706

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 0.645 in 152,064 control chromosomes in the GnomAD database, including 35,098 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 0.65 (35098 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.645 AC: 98071 AN: 151946 Hom.: 35100 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.645 AC: 98094 AN: 152064 Hom.: 35098 Cov.: 31 AF XY: 0.650 AC XY: 48348 AN XY: 74330

African (AFR) AF: 0.307 AC: 12728 AN: 41436

American (AMR) AF: 0.764 AC: 11688 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2859 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4501 AN: 5170

South Asian (SAS) AF: 0.848 AC: 4088 AN: 4822

European-Finnish (FIN) AF: 0.723 AC: 7640 AN: 10566

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.768 AC: 52214 AN: 67994

Other (OTH) AF: 0.694 AC: 1466 AN: 2112

Alfa AF: 0.743 Hom.: 62280

Bravo AF: 0.635

Asia WGS AF: 0.798 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.030
DANN	Benign	0.89
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2172706; hg19: chr1-154669294;