chr9-24769090-A-G

Position:

• chr9-24769090-A-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 0.02 in 152,332 control chromosomes in the GnomAD database, including 58 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 0.020 (58 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0200 AC: 3044 AN: 152214 Hom.: 58 Cov.: 32

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0200 AC: 3047 AN: 152332 Hom.: 58 Cov.: 32 AF XY: 0.0208 AC XY: 1548 AN XY: 74486

Gnomad4 AFR AF: 0.00568

Gnomad4 AMR AF: 0.0163

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.00958 Hom.: 0

Bravo AF: 0.0193

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79703820; hg19: chr9-24769088;