rs1982915

Positions:

• chr9-27579562-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 0.477 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.481

Alfa AF: 0.494 Hom.: 40121

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1982915; hg19: chr9-27579560;