rs553379

Variant names:

• chr11-98064519-T-A
• rs553379

Your query was ambiguous. Multiple possible variants found:

• chr11-98064519-T-A
• chr11-98064519-T-G

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 0.732 in 152,084 control chromosomes in the GnomAD database, including 40,969 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 0.73 (40969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.809 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: 0.732 AC: 111305 AN: 151966 Hom.: 40939 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.732 AC: 111386 AN: 152084 Hom.: 40969 Cov.: 32 AF XY: 0.730 AC XY: 54222 AN XY: 74318

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.735

Alfa AF: 0.744 Hom.: 5257

Bravo AF: 0.741

Asia WGS AF: 0.673 AC: 2344 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	0.68
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs553379; hg19: chr11-97935247;