9-88220811-T-C

Variant names:

• chr9-88220811-T-C
• rs2778031

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 0.605 in 152,108 control chromosomes in the GnomAD database, including 31,179 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 0.61 (31179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

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 (NFE) allele frequency at 95% confidence interval = 0.753 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: 0.606 AC: 92059 AN: 151990 Hom.: 31171 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.605 AC: 92081 AN: 152108 Hom.: 31179 Cov.: 32 AF XY: 0.608 AC XY: 45218 AN XY: 74386

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.669

Alfa AF: 0.731 Hom.: 48106

Bravo AF: 0.579

Asia WGS AF: 0.551 AC: 1912 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	1.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2778031; hg19: chr9-90835726;