14-53960339-T-G

Position:

• chr14-53960339-T-G

Variant summary

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

The XM_047432035.1(LOC124903317):​c.429-1522T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,984 control chromosomes in the GnomAD database, including 15,636 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 0.45 (15636 hom., cov: 32)
• Consequence: LOC124903317 XM_047432035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

LOC124903317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903317	XM_047432035.1	c.429-1522T>G		intron_variant			XP_047287991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287156	ENST00000667337.1	n.1659-1522T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68393 AN: 151866 Hom.: 15626 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.450 AC: 68448 AN: 151984 Hom.: 15636 Cov.: 32 AF XY: 0.451 AC XY: 33486 AN XY: 74264

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.480

Alfa AF: 0.473 Hom.: 4958

Bravo AF: 0.448

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4898820; hg19: chr14-54427057;