rs3814113

Positions:

• chr9-16915023-T-C

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 0.413 in 151,824 control chromosomes in the GnomAD database, including 14,020 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 0.41 (14020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62570 AN: 151706 Hom.: 13995 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.413 AC: 62647 AN: 151824 Hom.: 14020 Cov.: 31 AF XY: 0.414 AC XY: 30719 AN XY: 74198

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.417

Alfa AF: 0.342 Hom.: 21173

Bravo AF: 0.434

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814113; hg19: chr9-16915021; COSMIC: COSV53318135;