9-88196267-T-C

Variant names:

• chr9-88196267-T-C
• rs2814828

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.727 AC: 30140 AN: 41468

American (AMR) AF: 0.672 AC: 10256 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2833 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1935 AN: 5164

South Asian (SAS) AF: 0.673 AC: 3246 AN: 4824

European-Finnish (FIN) AF: 0.779 AC: 8247 AN: 10588

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51738 AN: 67988

Other (OTH) AF: 0.760 AC: 1606 AN: 2114

Alfa AF: 0.745 Hom.: 171644

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2814828; hg19: chr9-90811182;