1-17016288-G-T

Variant names:

• chr1-17016288-G-T
• rs11203280

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 0.412 in 152,048 control chromosomes in the GnomAD database, including 13,510 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 (13510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62505 AN: 151930 Hom.: 13482 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.412 AC: 62582 AN: 152048 Hom.: 13510 Cov.: 33 AF XY: 0.418 AC XY: 31101 AN XY: 74316

African (AFR) AF: 0.508 AC: 21079 AN: 41456

American (AMR) AF: 0.455 AC: 6948 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1413 AN: 3464

East Asian (EAS) AF: 0.646 AC: 3334 AN: 5158

South Asian (SAS) AF: 0.455 AC: 2194 AN: 4826

European-Finnish (FIN) AF: 0.374 AC: 3953 AN: 10564

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22336 AN: 67982

Other (OTH) AF: 0.425 AC: 899 AN: 2114

Alfa AF: 0.361 Hom.: 18022

Bravo AF: 0.422

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11203280; hg19: chr1-17342783;