ENST00000568496.2:n.3288C>T

Variant names:

• chr15-74369553-C-T
• rs2073475
• ENST00000568496.2:n.3288C>T

Variant summary

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

The ENST00000568496.2(ENSG00000261821):​n.3288C>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 0.28 in 152,162 control chromosomes in the GnomAD database, including 7,865 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 0.28 (7861 hom., cov: 32)
  • Exomes 𝑓: 0.25 (4 hom.)
• Consequence: ENSG00000261821 ENST00000568496.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903524	XR_007064709.1	n.3936C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261821	ENST00000568496.2	n.3288C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42516 AN: 152000 Hom.: 7831 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.250 AC: 11 AN: 44 Hom.: 4 Cov.: 0 AF XY: 0.214 AC XY: 6 AN XY: 28

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.280 AC: 42612 AN: 152118 Hom.: 7861 Cov.: 32 AF XY: 0.281 AC XY: 20904 AN XY: 74356

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.258

Alfa AF: 0.179 Hom.: 5750

Bravo AF: 0.293

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
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: rs2073475; hg19: chr15-74661894;