1-116738074-C-T

Variant names:

• chr1-116738074-C-T
• rs798000

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 0.721 in 151,110 control chromosomes in the GnomAD database, including 39,476 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 0.72 (39476 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.721 AC: 108849 AN: 151004 Hom.: 39435 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.721 AC: 108939 AN: 151110 Hom.: 39476 Cov.: 31 AF XY: 0.720 AC XY: 53151 AN XY: 73818

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.736

Alfa AF: 0.628 Hom.: 3280

Bravo AF: 0.729

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798000; hg19: chr1-117280696;