chr9-6351834-T-C

Variant names:

• chr9-6351834-T-C
• rs10975552

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;