rs11143679

Positions:

• chr9-73722598-C-T

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 0.412 in 151,936 control chromosomes in the GnomAD database, including 15,302 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 (15302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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: 0.412 AC: 62556 AN: 151818 Hom.: 15303 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.412 AC: 62561 AN: 151936 Hom.: 15302 Cov.: 31 AF XY: 0.417 AC XY: 30913 AN XY: 74220

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.472

Alfa AF: 0.443 Hom.: 2612

Bravo AF: 0.390

Asia WGS AF: 0.523 AC: 1813 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11143679; hg19: chr9-76337514;