rs2016167

Variant names:

• chr5-113714894-G-T
• rs2016167

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 0.203 in 152,178 control chromosomes in the GnomAD database, including 3,663 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 0.20 (3663 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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: 0.203 AC: 30934 AN: 152060 Hom.: 3662 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.203 AC: 30964 AN: 152178 Hom.: 3663 Cov.: 33 AF XY: 0.197 AC XY: 14653 AN XY: 74410

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0231

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.173

Alfa AF: 0.195 Hom.: 390

Bravo AF: 0.209

Asia WGS AF: 0.0630 AC: 219 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	0.90
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2016167; hg19: chr5-113050591;