rs4860568

Positions:

• chr4-64142664-G-A
• chr4-64142664-G-C

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 0.13 in 152,062 control chromosomes in the GnomAD database, including 1,375 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 (1375 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.130 AC: 19760 AN: 151942 Hom.: 1371 Cov.: 33

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.130 AC: 19765 AN: 152062 Hom.: 1375 Cov.: 33 AF XY: 0.131 AC XY: 9700 AN XY: 74318

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.143

Alfa AF: 0.128 Hom.: 191

Bravo AF: 0.131

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4860568; hg19: chr4-65008382;