14-81950927-C-G

Variant summary

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

The ENST00000554814.1(ENSG00000259035):n.316-79179C>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 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,830 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 0.39 (12830 hom., cov: 31)
• Consequence: ENST00000554814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984704	XR_007064292.1	n.842-123001C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554814.1	n.316-79179C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58749 AN: 151754 Hom.: 12782 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.388 AC: 58868 AN: 151870 Hom.: 12830 Cov.: 31 AF XY: 0.388 AC XY: 28770 AN XY: 74204

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.389

Alfa AF: 0.333 Hom.: 1181

Bravo AF: 0.401

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.81
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953408; hg19: chr14-82417271;