rs11569611

chr14-35406369-CAG-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The variant allele was found at a frequency of 0.0284 in 152,262 control chromosomes in the GnomAD database, including 100 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.028 (100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0284 (4320/152262) while in subpopulation NFE AF= 0.04 (2718/68030). AF 95% confidence interval is 0.0387. There are 100 homozygotes in gnomad4. There are 2201 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 100 gene

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: 0.0284 AC: 4320 AN: 152144 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.00572

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00496

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0284 AC: 4320 AN: 152262 Hom.: 100 Cov.: 32 AF XY: 0.0296 AC XY: 2201 AN XY: 74432

Gnomad4 AFR AF: 0.00570

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00497

Gnomad4 FIN AF: 0.0941

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0398 Hom.: 24

Bravo AF: 0.0223

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11569611; hg19: chr14-35875575;