chr1-186650720-A-G

Variant names:

• chr1-186650720-A-G
• rs718665

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 0.991 in 152,252 control chromosomes in the GnomAD database, including 74,807 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 0.99 (74807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 0 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 = 0.99 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: 0.991 AC: 150797 AN: 152134 Hom.: 74751 Cov.: 32

Gnomad AFR AF: 0.998

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.991 AC: 150912 AN: 152252 Hom.: 74807 Cov.: 32 AF XY: 0.991 AC XY: 73752 AN XY: 74454

African (AFR) AF: 0.998 AC: 41473 AN: 41540

American (AMR) AF: 0.995 AC: 15205 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 3386 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5178

South Asian (SAS) AF: 0.946 AC: 4569 AN: 4828

European-Finnish (FIN) AF: 0.997 AC: 10567 AN: 10596

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67281 AN: 68040

Other (OTH) AF: 0.987 AC: 2085 AN: 2112

Alfa AF: 0.991 Hom.: 9425

Bravo AF: 0.992

Asia WGS AF: 0.978 AC: 3399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.46
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs718665; hg19: chr1-186619852;