rs11669977

Positions:

• chr19-49060867-A-G

Variant summary

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

The ENST00000597865.1(ENSG00000268108):​n.255A>G 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 0.166 in 174,356 control chromosomes in the GnomAD database, including 2,592 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 0.17 (2286 hom., cov: 31)
  • Exomes 𝑓: 0.15 (306 hom.)
• Consequence: ENST00000597865.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTF4	XR_001753693.1	n.879+297T>C		intron_variant, non_coding_transcript_variant
NTF4	XR_001753694.1	n.880-58T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000597865.1	n.255A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25579 AN: 151806 Hom.: 2285 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.150 AC: 3354 AN: 22432 Hom.: 306 Cov.: 0 AF XY: 0.146 AC XY: 1683 AN XY: 11546

Gnomad4 AFR exome AF: 0.116

Gnomad4 AMR exome AF: 0.221

Gnomad4 ASJ exome AF: 0.145

Gnomad4 EAS exome AF: 0.128

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.149

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.168 AC: 25591 AN: 151924 Hom.: 2286 Cov.: 31 AF XY: 0.166 AC XY: 12316 AN XY: 74248

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.170

Alfa AF: 0.178 Hom.: 3369

Bravo AF: 0.177

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669977; hg19: chr19-49564124;