11-89304768-T-C

Variant names:

• chr11-89304768-T-C
• rs1806319

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 0.411 in 151,714 control chromosomes in the GnomAD database, including 13,833 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 (13833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.411 AC: 62335 AN: 151596 Hom.: 13802 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.411 AC: 62417 AN: 151714 Hom.: 13833 Cov.: 31 AF XY: 0.406 AC XY: 30122 AN XY: 74116

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.387

Alfa AF: 0.360 Hom.: 20266

Bravo AF: 0.416

Asia WGS AF: 0.296 AC: 1028 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1806319; hg19: chr11-89037936;