rs945246

Variant names:

• chr9-120111878-T-C
• rs945246

Your query was ambiguous. Multiple possible variants found:

• chr9-120111878-T-C
• chr9-120111878-T-G

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 0.553 in 152,118 control chromosomes in the GnomAD database, including 23,335 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 (23335 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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: 0.553 AC: 84000 AN: 152000 Hom.: 23311 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.553 AC: 84079 AN: 152118 Hom.: 23335 Cov.: 33 AF XY: 0.552 AC XY: 41038 AN XY: 74366

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.571

Alfa AF: 0.528 Hom.: 42431

Bravo AF: 0.562

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.40
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs945246; hg19: chr9-122874156; COSMIC: COSV60400430;