rs1353548

Positions:

• chr11-92037113-G-A

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 0.0441 in 152,072 control chromosomes in the GnomAD database, including 325 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 0.044 (325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0440 AC: 6691 AN: 151954 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.00950

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00978

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0441 AC: 6705 AN: 152072 Hom.: 325 Cov.: 32 AF XY: 0.0437 AC XY: 3247 AN XY: 74348

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0301

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.00952

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.0326

Gnomad4 NFE AF: 0.00978

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0197 Hom.: 55

Bravo AF: 0.0469

Asia WGS AF: 0.0120 AC: 43 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	1.1
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353548; hg19: chr11-91770279;