rs11943380

chr4-189295710-A-C

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 0.16 in 152,102 control chromosomes in the GnomAD database, including 2,782 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 0.16 (2782 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.160 AC: 24327 AN: 151984 Hom.: 2775 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.160 AC: 24370 AN: 152102 Hom.: 2782 Cov.: 33 AF XY: 0.157 AC XY: 11673 AN XY: 74348

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.162

Alfa AF: 0.116 Hom.: 930

Bravo AF: 0.168

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11943380; hg19: chr4-190216864;