9-88989548-T-G

Variant names:

• chr9-88989548-T-G
• rs7022797

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 0.382 in 151,968 control chromosomes in the GnomAD database, including 11,220 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 0.38 (11220 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.382 AC: 58042 AN: 151848 Hom.: 11214 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.382 AC: 58068 AN: 151968 Hom.: 11220 Cov.: 31 AF XY: 0.382 AC XY: 28342 AN XY: 74258

African (AFR) AF: 0.416 AC: 17233 AN: 41434

American (AMR) AF: 0.366 AC: 5597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1668 AN: 5154

South Asian (SAS) AF: 0.386 AC: 1847 AN: 4780

European-Finnish (FIN) AF: 0.325 AC: 3437 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25376 AN: 67964

Other (OTH) AF: 0.392 AC: 827 AN: 2112

Alfa AF: 0.328 Hom.: 1827

Bravo AF: 0.387

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7022797; hg19: chr9-91604463;