9-88989662-G-C

Variant names:

• chr9-88989662-G-C
• rs11137480

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 0.37 in 152,008 control chromosomes in the GnomAD database, including 10,428 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 0.37 (10428 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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: 0.370 AC: 56152 AN: 151890 Hom.: 10419 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.370 AC: 56178 AN: 152008 Hom.: 10428 Cov.: 31 AF XY: 0.370 AC XY: 27504 AN XY: 74294

African (AFR) AF: 0.372 AC: 15435 AN: 41456

American (AMR) AF: 0.361 AC: 5509 AN: 15274

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

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5150

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4816

European-Finnish (FIN) AF: 0.326 AC: 3446 AN: 10574

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

European-Non Finnish (NFE) AF: 0.373 AC: 25367 AN: 67958

Other (OTH) AF: 0.384 AC: 809 AN: 2108

Alfa AF: 0.362 Hom.: 1287

Bravo AF: 0.372

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs11137480; hg19: chr9-91604577;