1-218224238-A-G

Variant names:

• chr1-218224238-A-G
• rs1416156

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 0.655 in 152,050 control chromosomes in the GnomAD database, including 33,271 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 0.66 (33271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.655 AC: 99531 AN: 151932 Hom.: 33210 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.655 AC: 99649 AN: 152050 Hom.: 33271 Cov.: 32 AF XY: 0.659 AC XY: 48948 AN XY: 74286

African (AFR) AF: 0.724 AC: 30010 AN: 41460

American (AMR) AF: 0.741 AC: 11326 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2266 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4709 AN: 5168

South Asian (SAS) AF: 0.753 AC: 3630 AN: 4822

European-Finnish (FIN) AF: 0.561 AC: 5929 AN: 10564

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39486 AN: 67970

Other (OTH) AF: 0.678 AC: 1433 AN: 2114

Alfa AF: 0.613 Hom.: 123042

Bravo AF: 0.676

Asia WGS AF: 0.809 AC: 2812 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	1.1
DANN	Benign	0.77
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1416156; hg19: chr1-218397580; COSMIC: COSV60027916;