chr1-16115233-C-G

Position:

• chr1-16115233-C-G

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 0.129 in 152,238 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.130 AC: 19704 AN: 152120 Hom.: 1484 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.129 AC: 19702 AN: 152238 Hom.: 1484 Cov.: 32 AF XY: 0.124 AC XY: 9246 AN XY: 74452

Gnomad4 AFR AF: 0.0816

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.117

Alfa AF: 0.155 Hom.: 264

Bravo AF: 0.124

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11260867; hg19: chr1-16441728;