14-53589909-G-A

Position:

• chr14-53589909-G-A

Variant summary

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

The ENST00000648066.1(ENSG00000237356):​n.335-97290G>A 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 0.147 in 152,180 control chromosomes in the GnomAD database, including 1,920 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 0.15 (1920 hom., cov: 32)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370504	XR_943876.3	n.29701-97290G>A		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750974.1	n.3896-97290G>A		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750975.3	n.29701-97290G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648066.1	n.335-97290G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22315 AN: 152062 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.147 AC: 22307 AN: 152180 Hom.: 1920 Cov.: 32 AF XY: 0.143 AC XY: 10665 AN XY: 74402

Gnomad4 AFR AF: 0.0767

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.174

Alfa AF: 0.188 Hom.: 3872

Bravo AF: 0.140

Asia WGS AF: 0.0790 AC: 275 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	9.1
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: rs1001161; hg19: chr14-54056627;