chr1-16115233-C-G

Variant names:

• chr1-16115233-C-G
• rs11260867

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;