rs1123721

Variant names:

• chr9-136147543-A-G
• rs1123721

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 0.662 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.664 AC: 27563 AN: 41500

American (AMR) AF: 0.698 AC: 10677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3472

East Asian (EAS) AF: 0.652 AC: 3360 AN: 5152

South Asian (SAS) AF: 0.709 AC: 3416 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7522 AN: 10590

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43983 AN: 67986

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.659 Hom.: 4539

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1123721; hg19: chr9-139039389;