9-88196267-T-C

Position:

• chr9-88196267-T-C

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 152,086 control chromosomes in the GnomAD database, including 40,946 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 (40946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110767 AN: 151968 Hom.: 40905 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.729 AC: 110861 AN: 152086 Hom.: 40946 Cov.: 32 AF XY: 0.725 AC XY: 53953 AN XY: 74368

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.760

Alfa AF: 0.749 Hom.: 71951

Bravo AF: 0.723

Asia WGS AF: 0.563 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2814828; hg19: chr9-90811182;