9-6351834-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 0.343 in 151,792 control chromosomes in the GnomAD database, including 9,279 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 0.34 (9279 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

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 (NFE) allele frequency at 95% confidence interval = 0.375 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: 0.343 AC: 52018 AN: 151674 Hom.: 9277 Cov.: 30

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.343 AC: 52032 AN: 151792 Hom.: 9279 Cov.: 30 AF XY: 0.348 AC XY: 25786 AN XY: 74172

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.365

Alfa AF: 0.305 Hom.: 1748

Bravo AF: 0.335

Asia WGS AF: 0.274 AC: 953 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	1.0
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10975552; hg19: chr9-6351834;