9-103027310-G-C

Position:

• chr9-103027310-G-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 0.551 in 152,014 control chromosomes in the GnomAD database, including 24,525 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 0.55 (24525 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103027310G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83727 AN: 151896 Hom.: 24478 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.551 AC: 83826 AN: 152014 Hom.: 24525 Cov.: 33 AF XY: 0.555 AC XY: 41215 AN XY: 74280

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.576

Alfa AF: 0.494 Hom.: 2339

Bravo AF: 0.581

Asia WGS AF: 0.843 AC: 2928 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	1.7
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417706; hg19: chr9-105789592;