4-14142584-A-G

Variant names:

• chr4-14142584-A-G
• rs6844339
• ENST00000514339.1:n.156+88A>G

Variant summary

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

The ENST00000514339.1(ENSG00000251679):​n.156+88A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 145,320 control chromosomes in the GnomAD database, including 13,173 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 0.41 (13173 hom., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000251679 ENST00000514339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

ENSG00000251679 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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
ENSG00000251679	ENST00000514339.1	n.156+88A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.415 AC: 60228 AN: 145248 Hom.: 13165 Cov.: 24

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.415 AC: 60247 AN: 145320 Hom.: 13173 Cov.: 24 AF XY: 0.410 AC XY: 28845 AN XY: 70268

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.416

Alfa AF: 0.344 Hom.: 1807

Bravo AF: 0.418

Asia WGS AF: 0.280 AC: 962 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6844339; hg19: chr4-14144208;