1-16113897-C-T

Variant names:

• chr1-16113897-C-T
• rs7543472

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;