rs79703820

Variant names:

• chr9-24769090-A-G
• rs79703820

Your query was ambiguous. Multiple possible variants found:

• chr9-24769090-A-G
• chr9-24769090-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;