1-16113897-C-T

Position:

• chr1-16113897-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 0.738 in 151,324 control chromosomes in the GnomAD database, including 42,218 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 0.74 (42218 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 111625 AN: 151206 Hom.: 42207 Cov.: 28

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.792

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.738 AC: 111689 AN: 151324 Hom.: 42218 Cov.: 28 AF XY: 0.746 AC XY: 55126 AN XY: 73940

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.768

Alfa AF: 0.753 Hom.: 5397

Bravo AF: 0.731

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543472; hg19: chr1-16440392;