rs2378731

Positions:

• chr9-87330642-T-A

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 0.158 in 152,222 control chromosomes in the GnomAD database, including 2,168 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 0.16 (2168 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24032 AN: 152104 Hom.: 2165 Cov.: 33

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.158 AC: 24040 AN: 152222 Hom.: 2168 Cov.: 33 AF XY: 0.160 AC XY: 11944 AN XY: 74420

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.178

Alfa AF: 0.163 Hom.: 298

Bravo AF: 0.162

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378731; hg19: chr9-89945557;