9-38738492-C-G

Position:

• chr9-38738492-C-G

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 0.121 in 152,216 control chromosomes in the GnomAD database, including 1,186 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 0.12 (1186 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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 (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.121 AC: 18339 AN: 152098 Hom.: 1179 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.121 AC: 18382 AN: 152216 Hom.: 1186 Cov.: 33 AF XY: 0.121 AC XY: 9000 AN XY: 74402

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0930

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0364 Hom.: 31

Bravo AF: 0.124

Asia WGS AF: 0.0810 AC: 283 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	3.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11794651; hg19: chr9-38738489;