rs9578200

chr13-30769727-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 0.0957 in 152,226 control chromosomes in the GnomAD database, including 943 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 0.096 (943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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: 0.0958 AC: 14573 AN: 152108 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0957 AC: 14567 AN: 152226 Hom.: 943 Cov.: 32 AF XY: 0.0923 AC XY: 6871 AN XY: 74424

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.110

Alfa AF: 0.139 Hom.: 1470

Bravo AF: 0.0942

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.5
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: rs9578200; hg19: chr13-31343864;