5-8650219-C-T

Variant names:

• chr5-8650219-C-T
• rs200116

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 0.134 in 152,154 control chromosomes in the GnomAD database, including 1,634 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 (1634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.134 AC: 20381 AN: 152036 Hom.: 1634 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.134 AC: 20379 AN: 152154 Hom.: 1634 Cov.: 32 AF XY: 0.138 AC XY: 10236 AN XY: 74378

African (AFR) AF: 0.0664 AC: 2758 AN: 41540

American (AMR) AF: 0.131 AC: 2003 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1055 AN: 5154

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4822

European-Finnish (FIN) AF: 0.166 AC: 1763 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10121 AN: 67982

Other (OTH) AF: 0.149 AC: 315 AN: 2108

Alfa AF: 0.141 Hom.: 2107

Bravo AF: 0.126

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.43
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs200116; hg19: chr5-8650331;