14-20440194-A-G

Variant names:

• chr14-20440194-A-G
• rs11160682
• ENST00000553568.1:n.439-19A>G

Variant summary

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

The ENST00000555016.1(ENSG00000291038):​n.232-458A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,808 control chromosomes in the GnomAD database, including 11,408 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 0.38 (11399 hom., cov: 31)
  • Exomes 𝑓: 0.43 (9 hom.)
• Consequence: ENSG00000291038 ENST00000555016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

ENSG00000259162 (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 (SAS) allele frequency at 95% confidence interval = 0.519 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
ENSG00000259162	ENST00000553568.1	n.439-19A>G		intron_variant	Intron 6 of 9	6
ENSG00000291038	ENST00000555016.1	n.232-458A>G		intron_variant	Intron 2 of 2	3
ENSG00000291038	ENST00000687238.1	n.585-458A>G		intron_variant	Intron 3 of 7
ENSG00000291038	ENST00000700970.1	n.490-458A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58278 AN: 151568 Hom.: 11393 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 0.434 AC: 53 AN: 122 Hom.: 9 Cov.: 0 AF XY: 0.456 AC XY: 41 AN XY: 90

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.384 AC: 58322 AN: 151686 Hom.: 11399 Cov.: 31 AF XY: 0.389 AC XY: 28801 AN XY: 74114

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.406

Alfa AF: 0.383 Hom.: 10836

Bravo AF: 0.373

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11160682; hg19: chr14-20908353; COSMIC: COSV60727884;