rs11668477

Variant names:

• chr19-11084354-A-G
• rs11668477

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 0.33 in 152,078 control chromosomes in the GnomAD database, including 11,433 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 0.33 (11433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 49 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 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: 0.329 AC: 50064 AN: 151960 Hom.: 11402 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.330 AC: 50136 AN: 152078 Hom.: 11433 Cov.: 32 AF XY: 0.326 AC XY: 24246 AN XY: 74336

African (AFR) AF: 0.658 AC: 27281 AN: 41462

American (AMR) AF: 0.243 AC: 3713 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.153 AC: 792 AN: 5168

South Asian (SAS) AF: 0.205 AC: 992 AN: 4828

European-Finnish (FIN) AF: 0.194 AC: 2052 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13826 AN: 67980

Other (OTH) AF: 0.288 AC: 608 AN: 2108

Alfa AF: 0.235 Hom.: 24242

Bravo AF: 0.350

Asia WGS AF: 0.233 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs11668477; hg19: chr19-11195030;