1-17307077-G-T

Position:

• chr1-17307077-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 0.635 in 152,096 control chromosomes in the GnomAD database, including 30,888 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 0.63 (30888 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17307077G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96508 AN: 151978 Hom.: 30865 Cov.: 34

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.635 AC: 96577 AN: 152096 Hom.: 30888 Cov.: 34 AF XY: 0.635 AC XY: 47224 AN XY: 74338

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.635

Alfa AF: 0.388 Hom.: 458

Bravo AF: 0.638

Asia WGS AF: 0.743 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2477134; hg19: chr1-17633572;