rs4314620

Positions:

• chr8-127618344-C-A

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 152,092 control chromosomes in the GnomAD database, including 1,623 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 (1623 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127618344C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286266	ENST00000650971.1	n.390-11424C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19799 AN: 151974 Hom.: 1619 Cov.: 33

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.130 AC: 19813 AN: 152092 Hom.: 1623 Cov.: 33 AF XY: 0.135 AC XY: 10037 AN XY: 74322

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.132

Alfa AF: 0.159 Hom.: 2289

Bravo AF: 0.113

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	1.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4314620; hg19: chr8-128630589;