rs11668505

Variant names:

• chr19-47845106-A-G
• rs11668505

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 0.302 in 152,022 control chromosomes in the GnomAD database, including 7,941 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 0.30 (7941 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 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: 0.302 AC: 45852 AN: 151904 Hom.: 7939 Cov.: 30

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.302 AC: 45868 AN: 152022 Hom.: 7941 Cov.: 30 AF XY: 0.296 AC XY: 22022 AN XY: 74298

African (AFR) AF: 0.152 AC: 6312 AN: 41488

American (AMR) AF: 0.317 AC: 4832 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3468

East Asian (EAS) AF: 0.0940 AC: 487 AN: 5180

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4816

European-Finnish (FIN) AF: 0.326 AC: 3445 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27131 AN: 67950

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.364 Hom.: 7727

Bravo AF: 0.294

Asia WGS AF: 0.164 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.54
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11668505; hg19: chr19-48348363;