rs11653989

Variant names:

• chr17-77008131-A-T
• rs11653989

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0463 AC: 1922 AN: 41552

American (AMR) AF: 0.139 AC: 2117 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3468

East Asian (EAS) AF: 0.102 AC: 526 AN: 5164

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4822

European-Finnish (FIN) AF: 0.0616 AC: 653 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0687 AC: 4670 AN: 68008

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11653989; hg19: chr17-75004213;