9-36036597-T-C

Variant names:

• chr9-36036597-T-C
• rs10814325

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 0.231 in 166,954 control chromosomes in the GnomAD database, including 7,031 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 0.24 (6790 hom., cov: 31)
  • Exomes 𝑓: 0.13 (241 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.240 AC: 36521 AN: 152008 Hom.: 6751 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.132 AC: 1953 AN: 14828 Hom.: 241 Cov.: 0 AF XY: 0.126 AC XY: 978 AN XY: 7770

Gnomad4 AFR exome AF: 0.478

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.133

Gnomad4 EAS exome AF: 0.492

Gnomad4 SAS exome AF: 0.265

Gnomad4 FIN exome AF: 0.0966

Gnomad4 NFE exome AF: 0.0824

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.241 AC: 36623 AN: 152126 Hom.: 6790 Cov.: 31 AF XY: 0.246 AC XY: 18280 AN XY: 74372

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.229

Alfa AF: 0.0327 Hom.: 22

Bravo AF: 0.258

Asia WGS AF: 0.436 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10814325; hg19: chr9-36036594;