rs4754552

chr11-98862902-G-Achr11-98862902-G-C

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 0.601 in 152,000 control chromosomes in the GnomAD database, including 27,807 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 0.60 (27807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91323 AN: 151880 Hom.: 27805 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.601 AC: 91354 AN: 152000 Hom.: 27807 Cov.: 32 AF XY: 0.604 AC XY: 44895 AN XY: 74284

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.602

Alfa AF: 0.575 Hom.: 38684

Bravo AF: 0.605

Asia WGS AF: 0.572 AC: 1990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.74
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754552; hg19: chr11-98733632;