11-89157946-A-G

Variant names:

• chr11-89157946-A-G
• rs10830228

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 0.536 in 151,694 control chromosomes in the GnomAD database, including 22,377 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 (22377 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81224 AN: 151576 Hom.: 22377 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.536 AC: 81244 AN: 151694 Hom.: 22377 Cov.: 31 AF XY: 0.538 AC XY: 39848 AN XY: 74126

African (AFR) AF: 0.401 AC: 16618 AN: 41418

American (AMR) AF: 0.577 AC: 8766 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3488 AN: 5090

South Asian (SAS) AF: 0.664 AC: 3196 AN: 4814

European-Finnish (FIN) AF: 0.514 AC: 5435 AN: 10574

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39334 AN: 67840

Other (OTH) AF: 0.581 AC: 1223 AN: 2104

Alfa AF: 0.546 Hom.: 20336

Bravo AF: 0.538

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10830228; hg19: chr11-88891114;