rs1545527

Variant names:

• chr11-59486922-T-C
• rs1545527

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 0.301 in 152,086 control chromosomes in the GnomAD database, including 7,171 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 0.30 (7171 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 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: 0.301 AC: 45732 AN: 151968 Hom.: 7155 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.301 AC: 45795 AN: 152086 Hom.: 7171 Cov.: 32 AF XY: 0.297 AC XY: 22082 AN XY: 74352

African (AFR) AF: 0.353 AC: 14649 AN: 41462

American (AMR) AF: 0.215 AC: 3284 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1414 AN: 5172

South Asian (SAS) AF: 0.392 AC: 1889 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2580 AN: 10588

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19926 AN: 67982

Other (OTH) AF: 0.296 AC: 623 AN: 2106

Alfa AF: 0.300 Hom.: 11770

Bravo AF: 0.300

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.67
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1545527; hg19: chr11-59254395;