rs4868514

Variant names:

• chr5-175357866-G-A
• rs4868514

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 0.171 in 152,080 control chromosomes in the GnomAD database, including 2,367 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 0.17 (2367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.171 AC: 25924 AN: 151962 Hom.: 2361 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.171 AC: 25963 AN: 152080 Hom.: 2367 Cov.: 32 AF XY: 0.168 AC XY: 12513 AN XY: 74348

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.169

Alfa AF: 0.163 Hom.: 411

Bravo AF: 0.173

Asia WGS AF: 0.138 AC: 481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4868514; hg19: chr5-174784869;