9-88220811-T-C

Variant names:

• chr9-88220811-T-C
• rs2778031

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 0.605 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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.297 AC: 12306 AN: 41502

American (AMR) AF: 0.623 AC: 9515 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2745 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2185 AN: 5144

South Asian (SAS) AF: 0.673 AC: 3235 AN: 4806

European-Finnish (FIN) AF: 0.781 AC: 8275 AN: 10602

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51547 AN: 67992

Other (OTH) AF: 0.669 AC: 1408 AN: 2106

Alfa AF: 0.718 Hom.: 112232

Bravo AF: 0.579

Asia WGS AF: 0.551 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2778031; hg19: chr9-90835726;