9-88196267-T-C

Variant names:

• chr9-88196267-T-C
• rs2814828

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;