rs11260867

Variant names:

• chr1-16115233-C-G
• rs11260867

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 0.129 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0816 AC: 3391 AN: 41552

American (AMR) AF: 0.0966 AC: 1478 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1553 AN: 10610

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11963 AN: 67988

Other (OTH) AF: 0.117 AC: 246 AN: 2110

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
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs11260867; hg19: chr1-16441728;