1-234698385-A-G

Variant names:

• chr1-234698385-A-G
• rs11587639

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 0.0492 in 151,412 control chromosomes in the GnomAD database, including 211 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 0.049 (211 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0643 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: 0.0492 AC: 7437 AN: 151294 Hom.: 210 Cov.: 30

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0492 AC: 7456 AN: 151412 Hom.: 211 Cov.: 30 AF XY: 0.0496 AC XY: 3668 AN XY: 73924

African (AFR) AF: 0.0496 AC: 2045 AN: 41212

American (AMR) AF: 0.0677 AC: 1026 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3470

East Asian (EAS) AF: 0.0611 AC: 315 AN: 5156

South Asian (SAS) AF: 0.0317 AC: 151 AN: 4764

European-Finnish (FIN) AF: 0.0563 AC: 591 AN: 10490

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3115 AN: 67878

Other (OTH) AF: 0.0391 AC: 82 AN: 2096

Alfa AF: 0.0505 Hom.: 37

Bravo AF: 0.0514

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11587639; hg19: chr1-234834132;