chr11-13505086-T-C

Variant names:

• chr11-13505086-T-C
• rs11022858

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 0.541 in 151,876 control chromosomes in the GnomAD database, including 23,547 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 0.54 (23547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 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: 0.542 AC: 82186 AN: 151758 Hom.: 23539 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.541 AC: 82229 AN: 151876 Hom.: 23547 Cov.: 31 AF XY: 0.542 AC XY: 40231 AN XY: 74236

African (AFR) AF: 0.384 AC: 15904 AN: 41412

American (AMR) AF: 0.496 AC: 7565 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2420 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1534 AN: 5128

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6632 AN: 10542

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43474 AN: 67940

Other (OTH) AF: 0.553 AC: 1168 AN: 2112

Alfa AF: 0.584 Hom.: 18183

Bravo AF: 0.518

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.40
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11022858; hg19: chr11-13526633;