chr4-14142584-A-G

Position:

• chr4-14142584-A-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, non coding transcript 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: ENST00000514339.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000514339.1	n.156+88A>G		intron_variant, non_coding_transcript_variant		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;