rs11673198

Positions:

• chr19-46774455-C-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 0.217 in 151,572 control chromosomes in the GnomAD database, including 3,812 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 0.22 (3812 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46774455C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FKRP	ENST00000600646.5	n.248-2197C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32848 AN: 151452 Hom.: 3807 Cov.: 28

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.217 AC: 32876 AN: 151572 Hom.: 3812 Cov.: 28 AF XY: 0.222 AC XY: 16421 AN XY: 74040

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.216

Alfa AF: 0.191 Hom.: 385

Bravo AF: 0.229

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11673198; hg19: chr19-47277712;