chr1-17016288-G-T

Position:

• chr1-17016288-G-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 0.412 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;