9-97887977-A-T

Variant names:

• chr9-97887977-A-T
• rs7853349

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 0.498 in 151,924 control chromosomes in the GnomAD database, including 20,271 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 0.50 (20271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.498 AC: 75601 AN: 151806 Hom.: 20232 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.498 AC: 75684 AN: 151924 Hom.: 20271 Cov.: 31 AF XY: 0.505 AC XY: 37513 AN XY: 74258

African (AFR) AF: 0.658 AC: 27241 AN: 41420

American (AMR) AF: 0.493 AC: 7537 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3462

East Asian (EAS) AF: 0.835 AC: 4304 AN: 5152

South Asian (SAS) AF: 0.574 AC: 2761 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4790 AN: 10530

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26326 AN: 67942

Other (OTH) AF: 0.464 AC: 979 AN: 2108

Alfa AF: 0.447 Hom.: 2021

Bravo AF: 0.509

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7853349; hg19: chr9-100650259;