1-116720516-C-G

Variant names:

• chr1-116720516-C-G
• rs11586238

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 0.187 in 151,924 control chromosomes in the GnomAD database, including 2,954 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 0.19 (2954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.187 AC: 28390 AN: 151806 Hom.: 2954 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.187 AC: 28393 AN: 151924 Hom.: 2954 Cov.: 31 AF XY: 0.187 AC XY: 13894 AN XY: 74206

African (AFR) AF: 0.102 AC: 4222 AN: 41448

American (AMR) AF: 0.191 AC: 2909 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3468

East Asian (EAS) AF: 0.0451 AC: 232 AN: 5146

South Asian (SAS) AF: 0.234 AC: 1124 AN: 4804

European-Finnish (FIN) AF: 0.247 AC: 2601 AN: 10516

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15935 AN: 67966

Other (OTH) AF: 0.197 AC: 415 AN: 2104

Alfa AF: 0.208 Hom.: 451

Bravo AF: 0.177

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11586238; hg19: chr1-117263138;