rs1611114

Variant names:

• chr9-133635081-C-T
• rs1611114

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 0.313 in 152,106 control chromosomes in the GnomAD database, including 7,929 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 0.31 (7929 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.313 AC: 47521 AN: 151988 Hom.: 7934 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.313 AC: 47538 AN: 152106 Hom.: 7929 Cov.: 33 AF XY: 0.324 AC XY: 24065 AN XY: 74378

African (AFR) AF: 0.302 AC: 12504 AN: 41468

American (AMR) AF: 0.343 AC: 5239 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3456 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2281 AN: 4824

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17912 AN: 67986

Other (OTH) AF: 0.320 AC: 673 AN: 2106

Alfa AF: 0.275 Hom.: 7625

Bravo AF: 0.310

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.45
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1611114; hg19: chr9-136500203;