1-119430538-G-A

Variant names:

• chr1-119430538-G-A
• rs11579951

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 0.139 in 152,082 control chromosomes in the GnomAD database, including 2,056 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 0.14 (2056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.139 AC: 21056 AN: 151964 Hom.: 2052 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0687

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.139 AC: 21084 AN: 152082 Hom.: 2056 Cov.: 32 AF XY: 0.137 AC XY: 10222 AN XY: 74352

African (AFR) AF: 0.272 AC: 11276 AN: 41436

American (AMR) AF: 0.147 AC: 2241 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.0689 AC: 356 AN: 5170

South Asian (SAS) AF: 0.113 AC: 546 AN: 4818

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10594

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0792 AC: 5383 AN: 68002

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.110 Hom.: 163

Bravo AF: 0.153

Asia WGS AF: 0.107 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.7
DANN	Benign	0.89
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11579951; hg19: chr1-119973161;