rs11145506

chr9-77649668-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 0.0632 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;