chr9-97861095-G-A

Position:

• chr9-97861095-G-A

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 0.729 in 152,094 control chromosomes in the GnomAD database, including 41,743 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 0.73 (41743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.729 AC: 110734 AN: 151976 Hom.: 41690 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.729 AC: 110837 AN: 152094 Hom.: 41743 Cov.: 31 AF XY: 0.731 AC XY: 54375 AN XY: 74354

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.718

Alfa AF: 0.690 Hom.: 7577

Bravo AF: 0.743

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs993501; hg19: chr9-100623377;