4-11501980-G-A

Variant names:

• chr4-11501980-G-A
• rs1390096

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 0.228 in 151,996 control chromosomes in the GnomAD database, including 4,788 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 0.23 (4788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34650 AN: 151878 Hom.: 4779 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 34665 AN: 151996 Hom.: 4788 Cov.: 32 AF XY: 0.235 AC XY: 17484 AN XY: 74264

African (AFR) AF: 0.0826 AC: 3432 AN: 41528

American (AMR) AF: 0.232 AC: 3533 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2437 AN: 5154

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3645 AN: 10546

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18600 AN: 67930

Other (OTH) AF: 0.225 AC: 475 AN: 2108

Alfa AF: 0.256 Hom.: 12080

Bravo AF: 0.213

Asia WGS AF: 0.383 AC: 1330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.029
DANN	Benign	0.31
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1390096; hg19: chr4-11503604;