9-12344883-G-T

Variant names:

• chr9-12344883-G-T
• rs10756362

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 0.359 in 151,830 control chromosomes in the GnomAD database, including 10,606 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 0.36 (10606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.359 AC: 54513 AN: 151710 Hom.: 10604 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.359 AC: 54531 AN: 151830 Hom.: 10606 Cov.: 32 AF XY: 0.360 AC XY: 26733 AN XY: 74204

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.389

Alfa AF: 0.275 Hom.: 705

Bravo AF: 0.341

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10756362; hg19: chr9-12344883;