rs11930273

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;