rs11930273

Variant names:

• chr4-149980605-G-A
• rs11930273

Your query was ambiguous. Multiple possible variants found:

• chr4-149980605-G-A
• chr4-149980605-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0907

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.0813 Hom.: 1011

Bravo AF: 0.0973

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11930273; hg19: chr4-150901757;