rs1888701

chr9-12358097-T-C

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 0.872 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.879

Alfa AF: 0.906 Hom.: 7810

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

Splicing

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

Publications

LitVar

Other links and lift over

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