rs11143677

chr9-73720400-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.41 in 151,962 control chromosomes in the GnomAD database, including 15,186 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 0.41 (15186 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -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 = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62282 AN: 151842 Hom.: 15186 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.410 AC: 62289 AN: 151962 Hom.: 15186 Cov.: 33 AF XY: 0.415 AC XY: 30788 AN XY: 74266

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.469

Alfa AF: 0.440 Hom.: 2589

Bravo AF: 0.388

Asia WGS AF: 0.521 AC: 1798 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.74
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11143677; hg19: chr9-76335316;