rs2116714

Positions:

• chr5-148811835-G-A
• chr5-148811835-G-T

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 0.155 in 151,964 control chromosomes in the GnomAD database, including 4,881 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 0.16 (4881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 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: 0.155 AC: 23495 AN: 151846 Hom.: 4865 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.00587

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00852

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.155 AC: 23559 AN: 151964 Hom.: 4881 Cov.: 32 AF XY: 0.155 AC XY: 11497 AN XY: 74290

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.00587

Gnomad4 NFE AF: 0.00852

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0351 Hom.: 1243

Bravo AF: 0.173

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116714; hg19: chr5-148191398;