11-21599402-A-T

Variant names:

• chr11-21599402-A-T
• rs1573535

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 0.488 in 151,936 control chromosomes in the GnomAD database, including 18,684 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 0.49 (18684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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: 0.487 AC: 73994 AN: 151818 Hom.: 18641 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.488 AC: 74091 AN: 151936 Hom.: 18684 Cov.: 32 AF XY: 0.487 AC XY: 36136 AN XY: 74254

African (AFR) AF: 0.589 AC: 24362 AN: 41390

American (AMR) AF: 0.544 AC: 8295 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2816 AN: 5164

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29159 AN: 67974

Other (OTH) AF: 0.476 AC: 1002 AN: 2106

Alfa AF: 0.462 Hom.: 2071

Bravo AF: 0.508

Asia WGS AF: 0.489 AC: 1695 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1573535; hg19: chr11-21620948;