rs1424860

chr9-21073946-T-C

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/exons	MANE	UniProt

Ensembl

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