14-35478408-C-T

Position:

• chr14-35478408-C-T

Variant summary

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

The XR_943749.3(LOC105370450):​n.777-11G>A variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,016 control chromosomes in the GnomAD database, including 8,762 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 0.32 (8762 hom., cov: 32)
• Consequence: LOC105370450 XR_943749.3 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

LOC107984681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984681	XR_001750713.2	n.122+3279C>T		intron_variant, non_coding_transcript_variant
LOC105370450	XR_943749.3	n.777-11G>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48904 AN: 151898 Hom.: 8750 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.322 AC: 48963 AN: 152016 Hom.: 8762 Cov.: 32 AF XY: 0.324 AC XY: 24052 AN XY: 74310

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.312

Alfa AF: 0.245 Hom.: 2815

Bravo AF: 0.320

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10132268; hg19: chr14-35947614;