rs1476946

Variant names:

• chr9-111102469-C-T
• rs1476946

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.578 AC: 23947 AN: 41404

American (AMR) AF: 0.592 AC: 9043 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2765 AN: 5156

South Asian (SAS) AF: 0.554 AC: 2666 AN: 4814

European-Finnish (FIN) AF: 0.614 AC: 6491 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46539 AN: 67970

Other (OTH) AF: 0.621 AC: 1312 AN: 2114

Alfa AF: 0.663 Hom.: 111409

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1476946; hg19: chr9-113864749;