9-85503122-C-T

Variant names:

• chr9-85503122-C-T
• rs2378688

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 0.581 in 152,056 control chromosomes in the GnomAD database, including 25,859 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 0.58 (25859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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: 0.581 AC: 88339 AN: 151938 Hom.: 25841 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.581 AC: 88394 AN: 152056 Hom.: 25859 Cov.: 32 AF XY: 0.579 AC XY: 43022 AN XY: 74336

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.584

Alfa AF: 0.585 Hom.: 19030

Bravo AF: 0.585

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378688; hg19: chr9-88118037;