9-131574686-G-C

Variant names:

• chr9-131574686-G-C
• rs11243437

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 0.202 in 152,068 control chromosomes in the GnomAD database, including 3,723 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 0.20 (3723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 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: 0.202 AC: 30750 AN: 151948 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.202 AC: 30747 AN: 152068 Hom.: 3723 Cov.: 32 AF XY: 0.199 AC XY: 14801 AN XY: 74322

African (AFR) AF: 0.0893 AC: 3705 AN: 41508

American (AMR) AF: 0.185 AC: 2831 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3468

East Asian (EAS) AF: 0.104 AC: 539 AN: 5178

South Asian (SAS) AF: 0.137 AC: 662 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2911 AN: 10568

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19063 AN: 67936

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.138 Hom.: 281

Bravo AF: 0.192

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11243437; hg19: chr9-134450073;