chr1-229429985-A-G

Variant names:

• chr1-229429985-A-G
• rs499689

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 0.368 in 152,106 control chromosomes in the GnomAD database, including 10,537 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 0.37 (10537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 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: 0.368 AC: 55988 AN: 151988 Hom.: 10536 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.368 AC: 56000 AN: 152106 Hom.: 10537 Cov.: 32 AF XY: 0.365 AC XY: 27166 AN XY: 74334

African (AFR) AF: 0.291 AC: 12090 AN: 41510

American (AMR) AF: 0.393 AC: 6003 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3472

East Asian (EAS) AF: 0.311 AC: 1611 AN: 5178

South Asian (SAS) AF: 0.481 AC: 2322 AN: 4824

European-Finnish (FIN) AF: 0.332 AC: 3512 AN: 10570

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27745 AN: 67966

Other (OTH) AF: 0.384 AC: 812 AN: 2116

Alfa AF: 0.396 Hom.: 33929

Bravo AF: 0.366

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.014
DANN	Benign	0.32
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs499689; hg19: chr1-229565732;