1-229014074-G-A

Variant names:

• chr1-229014074-G-A
• rs10916407

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 0.293 in 143,464 control chromosomes in the GnomAD database, including 6,735 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 0.29 (6735 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.293 AC: 42037 AN: 143352 Hom.: 6728 Cov.: 27

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.293 AC: 42071 AN: 143464 Hom.: 6735 Cov.: 27 AF XY: 0.304 AC XY: 20926 AN XY: 68894

African (AFR) AF: 0.278 AC: 10800 AN: 38916

American (AMR) AF: 0.411 AC: 5623 AN: 13690

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 961 AN: 3428

East Asian (EAS) AF: 0.704 AC: 3495 AN: 4966

South Asian (SAS) AF: 0.480 AC: 2180 AN: 4546

European-Finnish (FIN) AF: 0.256 AC: 2168 AN: 8484

Middle Eastern (MID) AF: 0.331 AC: 78 AN: 236

European-Non Finnish (NFE) AF: 0.241 AC: 16017 AN: 66332

Other (OTH) AF: 0.302 AC: 595 AN: 1970

Alfa AF: 0.268 Hom.: 4334

Bravo AF: 0.291

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.1
DANN	Benign	0.86
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10916407; hg19: chr1-229149821;