1-116738074-C-T

Position:

• chr1-116738074-C-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 0.721 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/exons	MANE	UniProt

Ensembl

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