rs2553827

chr11-35075120-G-Achr11-35075120-G-T

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 0.59 in 152,038 control chromosomes in the GnomAD database, including 26,741 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 0.59 (26741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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: 0.590 AC: 89646 AN: 151922 Hom.: 26718 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.590 AC: 89710 AN: 152038 Hom.: 26741 Cov.: 33 AF XY: 0.595 AC XY: 44247 AN XY: 74320

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.620

Alfa AF: 0.562 Hom.: 2895

Bravo AF: 0.593

Asia WGS AF: 0.756 AC: 2621 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.18
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2553827; hg19: chr11-35096667;