11-65784486-A-G

Variant names:

• chr11-65784486-A-G
• rs479844

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 0.445 in 151,288 control chromosomes in the GnomAD database, including 16,848 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 0.44 (16848 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 77 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.445 AC: 67225 AN: 151168 Hom.: 16838 Cov.: 29

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.445 AC: 67257 AN: 151288 Hom.: 16848 Cov.: 29 AF XY: 0.449 AC XY: 33136 AN XY: 73848

African (AFR) AF: 0.221 AC: 9101 AN: 41180

American (AMR) AF: 0.398 AC: 6054 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1921 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1304 AN: 5096

South Asian (SAS) AF: 0.565 AC: 2707 AN: 4788

European-Finnish (FIN) AF: 0.622 AC: 6496 AN: 10442

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38033 AN: 67816

Other (OTH) AF: 0.470 AC: 985 AN: 2094

Alfa AF: 0.519 Hom.: 83897

Bravo AF: 0.411

Asia WGS AF: 0.376 AC: 1311 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	0.50
DANN	Benign	0.42
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs479844; hg19: chr11-65551957;