1-17016288-G-T

Variant names:

• chr1-17016288-G-T
• rs11203280

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 0.412 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.425

Alfa AF: 0.357 Hom.: 13347

Bravo AF: 0.422

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	-0.98
CADD	Benign	0.059
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11203280; hg19: chr1-17342783;