rs748923

Positions:

• chr11-13184613-C-A
• chr11-13184613-C-G

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 0.166 in 152,094 control chromosomes in the GnomAD database, including 2,802 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 0.17 (2802 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.166 AC: 25203 AN: 151976 Hom.: 2802 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0922

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.166 AC: 25226 AN: 152094 Hom.: 2802 Cov.: 32 AF XY: 0.172 AC XY: 12803 AN XY: 74344

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0530

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0973 Hom.: 1240

Bravo AF: 0.161

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748923; hg19: chr11-13206160;