9-31077303-C-T

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 0.0517 in 151,566 control chromosomes in the GnomAD database, including 363 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 0.052 (363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.0518 AC: 7844 AN: 151450 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0291

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0517 AC: 7843 AN: 151566 Hom.: 363 Cov.: 32 AF XY: 0.0548 AC XY: 4060 AN XY: 74084

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.00954 Hom.: 2

Bravo AF: 0.0560

Asia WGS AF: 0.128 AC: 443 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511874; hg19: chr9-31077301;