rs3824872

Variant names:

• chr11-45884054-A-C
• rs3824872

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 0.634 in 152,152 control chromosomes in the GnomAD database, including 34,390 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 0.63 (34390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 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: 0.635 AC: 96485 AN: 152034 Hom.: 34383 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.634 AC: 96527 AN: 152152 Hom.: 34390 Cov.: 33 AF XY: 0.636 AC XY: 47290 AN XY: 74382

African (AFR) AF: 0.302 AC: 12536 AN: 41472

American (AMR) AF: 0.675 AC: 10328 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2045 AN: 5160

South Asian (SAS) AF: 0.773 AC: 3725 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8142 AN: 10606

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54379 AN: 68004

Other (OTH) AF: 0.665 AC: 1406 AN: 2114

Alfa AF: 0.739 Hom.: 117491

Bravo AF: 0.610

Asia WGS AF: 0.647 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3824872; hg19: chr11-45905605;