rs11089637

Variant names:

• chr22-21624807-T-C
• rs11089637

Your query was ambiguous. Multiple possible variants found:

• chr22-21624807-T-C
• chr22-21624807-T-G

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 0.284 in 151,976 control chromosomes in the GnomAD database, including 7,451 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 0.28 (7451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 57 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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: 0.283 AC: 43017 AN: 151858 Hom.: 7410 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.284 AC: 43112 AN: 151976 Hom.: 7451 Cov.: 32 AF XY: 0.294 AC XY: 21833 AN XY: 74280

African (AFR) AF: 0.436 AC: 18064 AN: 41410

American (AMR) AF: 0.338 AC: 5159 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2616 AN: 5154

South Asian (SAS) AF: 0.385 AC: 1854 AN: 4818

European-Finnish (FIN) AF: 0.291 AC: 3075 AN: 10558

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10911 AN: 67974

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.211 Hom.: 11666

Bravo AF: 0.295

Asia WGS AF: 0.494 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11089637; hg19: chr22-21979096;