rs9318407

Variant names:

• chr13-76185864-C-G
• rs9318407

Your query was ambiguous. Multiple possible variants found:

• chr13-76185864-C-G
• chr13-76185864-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 0.131 in 152,046 control chromosomes in the GnomAD database, including 1,611 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 0.13 (1611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.131 AC: 19957 AN: 151928 Hom.: 1610 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.131 AC: 19957 AN: 152046 Hom.: 1611 Cov.: 32 AF XY: 0.132 AC XY: 9773 AN XY: 74290

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0696

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.137

Alfa AF: 0.152 Hom.: 273

Bravo AF: 0.120

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
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: rs9318407; hg19: chr13-76760000;