rs16968477

Positions:

• chr15-74370046-C-T

Variant summary

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

The ENST00000568496.2(ENSG00000261821):​n.3781C>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 0.232 in 152,026 control chromosomes in the GnomAD database, including 5,174 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 0.23 (5174 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENST00000568496.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903524	XR_007064709.1	n.4429C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568496.2	n.3781C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35130 AN: 151898 Hom.: 5151 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.232 AC: 35214 AN: 152016 Hom.: 5174 Cov.: 32 AF XY: 0.230 AC XY: 17097 AN XY: 74312

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.216

Alfa AF: 0.162 Hom.: 4834

Bravo AF: 0.242

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16968477; hg19: chr15-74662387;