rs2116787

Variant names:

• chr5-157072970-A-G
• rs2116787

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 0.136 in 152,180 control chromosomes in the GnomAD database, including 1,675 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 0.14 (1675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20609 AN: 152060 Hom.: 1670 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.136 AC: 20622 AN: 152180 Hom.: 1675 Cov.: 32 AF XY: 0.137 AC XY: 10186 AN XY: 74390

African (AFR) AF: 0.0664 AC: 2756 AN: 41518

American (AMR) AF: 0.228 AC: 3483 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 550 AN: 3472

East Asian (EAS) AF: 0.120 AC: 625 AN: 5190

South Asian (SAS) AF: 0.145 AC: 702 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1754 AN: 10594

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10286 AN: 68006

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.150 Hom.: 4568

Bravo AF: 0.141

Asia WGS AF: 0.138 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2116787; hg19: chr5-156499981;