rs3913107

chr9-27623560-G-Achr9-27623560-G-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 0.886 in 151,980 control chromosomes in the GnomAD database, including 59,780 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 0.89 (59780 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.886 AC: 134558 AN: 151862 Hom.: 59757 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.886 AC: 134629 AN: 151980 Hom.: 59780 Cov.: 31 AF XY: 0.886 AC XY: 65803 AN XY: 74302

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.889

Alfa AF: 0.896 Hom.: 27917

Bravo AF: 0.884

Asia WGS AF: 0.908 AC: 3134 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.6
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3913107; hg19: chr9-27623558;