9-111102370-C-T

Position:

• chr9-111102370-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 0.717 in 152,136 control chromosomes in the GnomAD database, including 40,259 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 0.72 (40259 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.111102370C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.717 AC: 109024 AN: 152018 Hom.: 40194 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.717 AC: 109144 AN: 152136 Hom.: 40259 Cov.: 32 AF XY: 0.720 AC XY: 53509 AN XY: 74364

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.711

Alfa AF: 0.653 Hom.: 16262

Bravo AF: 0.724

Asia WGS AF: 0.782 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491533; hg19: chr9-113864650;