rs11943380

Variant names:

• chr4-189295710-A-C
• rs11943380

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 0.16 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.320 AC: 13263 AN: 41452

American (AMR) AF: 0.120 AC: 1826 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0671 AC: 323 AN: 4816

European-Finnish (FIN) AF: 0.100 AC: 1059 AN: 10594

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.0992 AC: 6747 AN: 67994

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.119 Hom.: 1140

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
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs11943380; hg19: chr4-190216864;