9-27769783-C-G

Variant names:

• chr9-27769783-C-G
• rs1330197

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 0.929 in 152,106 control chromosomes in the GnomAD database, including 66,249 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 0.93 (66249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.930 AC: 141284 AN: 151988 Hom.: 66226 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.929 AC: 141361 AN: 152106 Hom.: 66249 Cov.: 32 AF XY: 0.929 AC XY: 69097 AN XY: 74368

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.940

Alfa AF: 0.973 Hom.: 3458

Bravo AF: 0.924

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330197; hg19: chr9-27769781;