chr9-88258738-G-A

Variant names:

• chr9-88258738-G-A
• rs10746837

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 0.487 in 152,062 control chromosomes in the GnomAD database, including 19,081 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 0.49 (19081 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73979 AN: 151944 Hom.: 19082 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.487 AC: 73998 AN: 152062 Hom.: 19081 Cov.: 33 AF XY: 0.485 AC XY: 36049 AN XY: 74328

African (AFR) AF: 0.361 AC: 14993 AN: 41486

American (AMR) AF: 0.417 AC: 6361 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5158

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4816

European-Finnish (FIN) AF: 0.576 AC: 6087 AN: 10568

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38970 AN: 67988

Other (OTH) AF: 0.534 AC: 1127 AN: 2110

Alfa AF: 0.546 Hom.: 25723

Bravo AF: 0.468

Asia WGS AF: 0.394 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.6
DANN	Benign	0.74
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10746837; hg19: chr9-90873653;