chr9-27579562-A-G

Variant names:

• chr9-27579562-A-G
• rs1982915

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 0.477 in 151,954 control chromosomes in the GnomAD database, including 17,736 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 0.48 (17736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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: 0.477 AC: 72465 AN: 151836 Hom.: 17724 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.477 AC: 72507 AN: 151954 Hom.: 17736 Cov.: 32 AF XY: 0.470 AC XY: 34947 AN XY: 74280

African (AFR) AF: 0.528 AC: 21881 AN: 41414

American (AMR) AF: 0.369 AC: 5636 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1138 AN: 5174

South Asian (SAS) AF: 0.385 AC: 1857 AN: 4822

European-Finnish (FIN) AF: 0.474 AC: 4997 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33839 AN: 67948

Other (OTH) AF: 0.481 AC: 1015 AN: 2112

Alfa AF: 0.492 Hom.: 61633

Bravo AF: 0.472

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs1982915; hg19: chr9-27579560;