4-149980605-G-A

Variant names:

• chr4-149980605-G-A
• rs11930273

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 0.0909 in 152,042 control chromosomes in the GnomAD database, including 804 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 0.091 (804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.0909 AC: 13816 AN: 151924 Hom.: 805 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0909 AC: 13823 AN: 152042 Hom.: 804 Cov.: 32 AF XY: 0.0904 AC XY: 6716 AN XY: 74300

African (AFR) AF: 0.0943 AC: 3912 AN: 41488

American (AMR) AF: 0.116 AC: 1763 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1555 AN: 5142

South Asian (SAS) AF: 0.0733 AC: 352 AN: 4800

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10584

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5067 AN: 67984

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.0845 Hom.: 2179

Bravo AF: 0.0973

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.78
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs11930273; hg19: chr4-150901757;