rs4903399

Positions:

• chr14-76308859-C-T

Variant summary

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

The ENST00000555465.1(ENSG00000258402):​n.242+966G>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 0.16 in 152,006 control chromosomes in the GnomAD database, including 2,180 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 0.16 (2180 hom., cov: 32)
• Consequence: ENST00000555465.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370575	XR_001750833.3	n.595+966G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555465.1	n.242+966G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24370 AN: 151888 Hom.: 2182 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.160 AC: 24370 AN: 152006 Hom.: 2180 Cov.: 32 AF XY: 0.160 AC XY: 11850 AN XY: 74292

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.192

Alfa AF: 0.197 Hom.: 4209

Bravo AF: 0.157

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4903399; hg19: chr14-76775202;