1-16113897-C-T

Variant names:

• chr1-16113897-C-T
• rs7543472

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.557 AC: 22882 AN: 41056

American (AMR) AF: 0.828 AC: 12639 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2684 AN: 3468

East Asian (EAS) AF: 0.964 AC: 4944 AN: 5128

South Asian (SAS) AF: 0.809 AC: 3885 AN: 4800

European-Finnish (FIN) AF: 0.833 AC: 8713 AN: 10462

Middle Eastern (MID) AF: 0.790 AC: 229 AN: 290

European-Non Finnish (NFE) AF: 0.785 AC: 53290 AN: 67850

Other (OTH) AF: 0.768 AC: 1613 AN: 2100

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7543472; hg19: chr1-16440392;