rs1888701

Variant names:

• chr9-12358097-T-C
• rs1888701

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 0.872 in 152,168 control chromosomes in the GnomAD database, including 58,519 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 0.87 (58519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.872 AC: 132585 AN: 152050 Hom.: 58491 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.872 AC: 132662 AN: 152168 Hom.: 58519 Cov.: 32 AF XY: 0.869 AC XY: 64646 AN XY: 74384

African (AFR) AF: 0.740 AC: 30694 AN: 41482

American (AMR) AF: 0.932 AC: 14253 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3140 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3912 AN: 5162

South Asian (SAS) AF: 0.809 AC: 3894 AN: 4816

European-Finnish (FIN) AF: 0.912 AC: 9668 AN: 10596

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64081 AN: 68028

Other (OTH) AF: 0.879 AC: 1858 AN: 2114

Alfa AF: 0.900 Hom.: 8020

Bravo AF: 0.867

Asia WGS AF: 0.777 AC: 2702 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	1.7
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1888701; hg19: chr9-12358097; COSMIC: COSV69448128;