rs11722989

Variant names:

• chr4-10124515-A-G
• rs11722989

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 0.445 in 152,074 control chromosomes in the GnomAD database, including 15,384 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 0.45 (15384 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.529 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: 0.445 AC: 67647 AN: 151956 Hom.: 15366 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.445 AC: 67698 AN: 152074 Hom.: 15384 Cov.: 33 AF XY: 0.448 AC XY: 33272 AN XY: 74334

African (AFR) AF: 0.354 AC: 14664 AN: 41470

American (AMR) AF: 0.539 AC: 8245 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2577 AN: 5164

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4822

European-Finnish (FIN) AF: 0.470 AC: 4969 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32126 AN: 67978

Other (OTH) AF: 0.445 AC: 940 AN: 2110

Alfa AF: 0.463 Hom.: 2843

Bravo AF: 0.445

Asia WGS AF: 0.437 AC: 1523 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	2.8
DANN	Benign	0.52
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11722989; hg19: chr4-10126139;