rs4314620

Variant names:

• chr8-127618344-C-A
• rs4314620
• ENST00000650971.1:n.390-11424C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650971.1(ENSG00000286266):​n.390-11424C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000286266 ENST00000650971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

ENSG00000286266 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286266	ENST00000650971.1	n.390-11424C>A		intron_variant	Intron 2 of 4

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;