1-63026691-A-T

Position:

• chr1-63026691-A-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 0.69 in 152,064 control chromosomes in the GnomAD database, including 36,983 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 0.69 (36983 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63026691A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104877 AN: 151944 Hom.: 36959 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.690 AC: 104960 AN: 152064 Hom.: 36983 Cov.: 32 AF XY: 0.679 AC XY: 50508 AN XY: 74336

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.721

Alfa AF: 0.591 Hom.: 1788

Bravo AF: 0.714

Asia WGS AF: 0.539 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11811517; hg19: chr1-63492362;