rs11145506

Variant names:

• chr9-77649668-C-T
• rs11145506

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 0.0632 in 152,186 control chromosomes in the GnomAD database, including 656 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 0.063 (656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 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: 0.0632 AC: 9612 AN: 152068 Hom.: 654 Cov.: 33

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0632 AC: 9611 AN: 152186 Hom.: 656 Cov.: 33 AF XY: 0.0711 AC XY: 5289 AN XY: 74402

Gnomad4 AFR AF: 0.0726

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0264 Hom.: 368

Bravo AF: 0.0672

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.66
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11145506; hg19: chr9-80264584;