1-169644556-A-G

Variant names:

• chr1-169644556-A-G
• rs10919202

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 0.22 in 152,052 control chromosomes in the GnomAD database, including 4,396 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 0.22 (4396 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.220 AC: 33356 AN: 151934 Hom.: 4365 Cov.: 30

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0817

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33434 AN: 152052 Hom.: 4396 Cov.: 30 AF XY: 0.221 AC XY: 16456 AN XY: 74324

African (AFR) AF: 0.355 AC: 14685 AN: 41424

American (AMR) AF: 0.211 AC: 3227 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3470

East Asian (EAS) AF: 0.0815 AC: 422 AN: 5176

South Asian (SAS) AF: 0.240 AC: 1154 AN: 4814

European-Finnish (FIN) AF: 0.200 AC: 2115 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10678 AN: 67988

Other (OTH) AF: 0.212 AC: 446 AN: 2108

Alfa AF: 0.174 Hom.: 4352

Bravo AF: 0.226

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.42
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs10919202; hg19: chr1-169613794;