14-77031632-C-A

Position:

• chr14-77031632-C-A

Variant summary

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

The NR_169510.1(LOC105370579):​n.1951G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,034 control chromosomes in the GnomAD database, including 57,524 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 0.87 (57523 hom., cov: 31)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: LOC105370579 NR_169510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370579	NR_169510.1	n.1951G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000693076.1	n.1626G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132083 AN: 151912 Hom.: 57495 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.859

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.869 AC: 132167 AN: 152030 Hom.: 57523 Cov.: 31 AF XY: 0.867 AC XY: 64465 AN XY: 74332

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.858

Alfa AF: 0.882 Hom.: 35827

Bravo AF: 0.864

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs183266; hg19: chr14-77497975;