rs1476946

Positions:

• chr9-111102469-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 0.629 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;