chr14-53353259-A-G

Position:

• chr14-53353259-A-G

Variant summary

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

The ENST00000435322.1(ENSG00000237356):​n.520-16196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,206 control chromosomes in the GnomAD database, including 57,686 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 0.87 (57686 hom., cov: 32)
• Consequence: ENSG00000237356 ENST00000435322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

ENSG00000237356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370504	XR_001750975.3	n.29650+2958A>G		intron_variant
LOC105370504	XR_007064173.1	n.29650+2958A>G		intron_variant
LOC105370504	XR_007064175.1	n.29650+2958A>G		intron_variant
LOC105370504	XR_943876.3	n.29650+2958A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237356	ENST00000435322.1	n.520-16196A>G		intron_variant		4
ENSG00000237356	ENST00000456100.6	n.276-16193A>G		intron_variant		4
ENSG00000237356	ENST00000648066.1	n.285-16193A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131690 AN: 152088 Hom.: 57669 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.866 AC: 131761 AN: 152206 Hom.: 57686 Cov.: 32 AF XY: 0.868 AC XY: 64606 AN XY: 74424

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.881

Alfa AF: 0.916 Hom.: 27066

Bravo AF: 0.854

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1255309; hg19: chr14-53819977;