rs1353548

Variant names:

• chr11-92037113-G-A
• rs1353548

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 0.0441 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
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.116 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: 0.0440 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

African (AFR) AF: 0.119 AC: 4919 AN: 41484

American (AMR) AF: 0.0301 AC: 459 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3466

East Asian (EAS) AF: 0.00952 AC: 49 AN: 5148

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4828

European-Finnish (FIN) AF: 0.0326 AC: 346 AN: 10598

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00978 AC: 665 AN: 67972

Other (OTH) AF: 0.0274 AC: 58 AN: 2114

Alfa AF: 0.0206 Hom.: 83

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1353548; hg19: chr11-91770279;