chr9-111102469-C-T

Variant names:

• chr9-111102469-C-T
• rs1476946

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 0.629 in 151,988 control chromosomes in the GnomAD database, including 30,325 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 0.63 (30325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95522 AN: 151870 Hom.: 30294 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.629 AC: 95599 AN: 151988 Hom.: 30325 Cov.: 32 AF XY: 0.623 AC XY: 46268 AN XY: 74300

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.621

Alfa AF: 0.665 Hom.: 48730

Bravo AF: 0.624

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
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: rs1476946; hg19: chr9-113864749;