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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00568 AC: 236 AN: 41580

American (AMR) AF: 0.0163 AC: 250 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.0657 AC: 317 AN: 4826

European-Finnish (FIN) AF: 0.0106 AC: 113 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0259 AC: 1760 AN: 68038

Other (OTH) AF: 0.0298 AC: 63 AN: 2116

Alfa AF: 0.0239 Hom.: 79

Bravo AF: 0.0193

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.87
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs79703820; hg19: chr9-24769088;