rs11569611

Variant names:

• chr14-35406369-CAG-C
• rs11569611
• ENST00000848537.1:n.241+2983_241+2984delAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000848537.1(ENSG00000310246):​n.241+2983_241+2984delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 1 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 100 gene

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
ENSG00000310246	ENST00000848537.1	n.241+2983_241+2984delAG		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00570 AC: 237 AN: 41562

American (AMR) AF: 0.0169 AC: 258 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.00497 AC: 24 AN: 4832

European-Finnish (FIN) AF: 0.0941 AC: 994 AN: 10568

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0400 AC: 2718 AN: 68030

Other (OTH) AF: 0.0194 AC: 41 AN: 2114

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11569611; hg19: chr14-35875575;