chr9-123300786-G-A

Variant names:

• chr9-123300786-G-A
• rs10985950

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 0.499 in 151,838 control chromosomes in the GnomAD database, including 19,743 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 0.50 (19743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75778 AN: 151720 Hom.: 19727 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.499 AC: 75833 AN: 151838 Hom.: 19743 Cov.: 31 AF XY: 0.500 AC XY: 37079 AN XY: 74186

African (AFR) AF: 0.352 AC: 14569 AN: 41384

American (AMR) AF: 0.509 AC: 7758 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2311 AN: 5144

South Asian (SAS) AF: 0.686 AC: 3296 AN: 4806

European-Finnish (FIN) AF: 0.498 AC: 5255 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38840 AN: 67942

Other (OTH) AF: 0.484 AC: 1016 AN: 2100

Alfa AF: 0.550 Hom.: 99021

Bravo AF: 0.492

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10985950; hg19: chr9-126063065;