rs1779308

Variant names:

• chr9-88835042-A-G
• rs1779308

Your query was ambiguous. Multiple possible variants found:

• chr9-88835042-A-G
• chr9-88835042-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 0.744 in 152,038 control chromosomes in the GnomAD database, including 42,329 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 0.74 (42329 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.744 AC: 113049 AN: 151922 Hom.: 42280 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.744 AC: 113156 AN: 152038 Hom.: 42329 Cov.: 31 AF XY: 0.744 AC XY: 55272 AN XY: 74324

African (AFR) AF: 0.807 AC: 33447 AN: 41438

American (AMR) AF: 0.725 AC: 11082 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2612 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4287 AN: 5180

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4820

European-Finnish (FIN) AF: 0.690 AC: 7282 AN: 10560

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48301 AN: 67968

Other (OTH) AF: 0.739 AC: 1563 AN: 2114

Alfa AF: 0.733 Hom.: 10889

Bravo AF: 0.755

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.19
DANN	Benign	0.47
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs1779308; hg19: chr9-91449957;