9-1162143-G-A

Variant names:

• chr9-1162143-G-A
• rs10511429

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 0.516 in 151,976 control chromosomes in the GnomAD database, including 20,871 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 0.52 (20871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78312 AN: 151858 Hom.: 20839 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.516 AC: 78397 AN: 151976 Hom.: 20871 Cov.: 32 AF XY: 0.525 AC XY: 39028 AN XY: 74286

African (AFR) AF: 0.582 AC: 24113 AN: 41446

American (AMR) AF: 0.550 AC: 8396 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3917 AN: 5178

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6478 AN: 10550

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29828 AN: 67946

Other (OTH) AF: 0.506 AC: 1070 AN: 2114

Alfa AF: 0.483 Hom.: 6711

Bravo AF: 0.514

Asia WGS AF: 0.692 AC: 2407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10511429; hg19: chr9-1162143;