rs1123721

chr9-136147543-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.662 in 152,134 control chromosomes in the GnomAD database, including 33,362 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 0.66 (33362 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100596 AN: 152016 Hom.: 33321 Cov.: 34

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.662 AC: 100696 AN: 152134 Hom.: 33362 Cov.: 34 AF XY: 0.668 AC XY: 49644 AN XY: 74352

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.676

Alfa AF: 0.660 Hom.: 4379

Bravo AF: 0.660

Asia WGS AF: 0.727 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1123721; hg19: chr9-139039389;