1-236132779-A-G

Variant names:

• chr1-236132779-A-G
• rs6689258

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 0.607 in 152,046 control chromosomes in the GnomAD database, including 28,828 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 0.61 (28828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 4 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 = 0.916 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: 0.607 AC: 92182 AN: 151928 Hom.: 28787 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.607 AC: 92279 AN: 152046 Hom.: 28828 Cov.: 32 AF XY: 0.614 AC XY: 45647 AN XY: 74320

African (AFR) AF: 0.679 AC: 28166 AN: 41458

American (AMR) AF: 0.685 AC: 10462 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1951 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4838 AN: 5160

South Asian (SAS) AF: 0.754 AC: 3639 AN: 4826

European-Finnish (FIN) AF: 0.553 AC: 5847 AN: 10580

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35345 AN: 67962

Other (OTH) AF: 0.629 AC: 1328 AN: 2110

Alfa AF: 0.557 Hom.: 12356

Bravo AF: 0.624

Asia WGS AF: 0.839 AC: 2922 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	4.1
DANN	Benign	0.58
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs6689258; hg19: chr1-236296079;