rs948016

Variant names:

• chr11-93636139-C-A
• rs948016

Your query was ambiguous. Multiple possible variants found:

• chr11-93636139-C-A
• chr11-93636139-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 0.414 in 151,986 control chromosomes in the GnomAD database, including 14,023 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 0.41 (14023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 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: 0.414 AC: 62847 AN: 151868 Hom.: 14013 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.414 AC: 62869 AN: 151986 Hom.: 14023 Cov.: 33 AF XY: 0.416 AC XY: 30892 AN XY: 74272

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.408

Alfa AF: 0.463 Hom.: 9867

Bravo AF: 0.418

Asia WGS AF: 0.442 AC: 1538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948016; hg19: chr11-93369305;