rs11653989

Positions:

• chr17-77008131-A-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 0.0697 in 152,196 control chromosomes in the GnomAD database, including 458 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 0.070 (458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10577 AN: 152078 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0697 AC: 10613 AN: 152196 Hom.: 458 Cov.: 32 AF XY: 0.0713 AC XY: 5302 AN XY: 74394

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0616

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0679 Hom.: 220

Bravo AF: 0.0746

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11653989; hg19: chr17-75004213;