rs1424860

Variant names:

• chr9-21073946-T-C
• rs1424860

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 0.122 in 152,182 control chromosomes in the GnomAD database, including 1,221 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 0.12 (1221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.122 AC: 18519 AN: 152064 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.122 AC: 18527 AN: 152182 Hom.: 1221 Cov.: 32 AF XY: 0.120 AC XY: 8951 AN XY: 74410

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.135

Alfa AF: 0.125 Hom.: 2142

Bravo AF: 0.124

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424860; hg19: chr9-21073945; COSMIC: COSV66525661;