ENST00000557528.1:n.48C>T

Variant names:

• chr15-20352408-C-T
• rs1039353
• ENST00000557528.1:n.48C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557528.1(ENSG00000258654):​n.48C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.42 (2117 hom., cov: 98)
  • Exomes 𝑓: 0.40 (93 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000258654 ENST00000557528.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 1 publications found

Genes affected

ENSG00000258654 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557528.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258654	ENST00000557528.1	TSL:5	n.48C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000258654	ENST00000554815.1	TSL:5	n.134+2957C>T		intron	N/A
	ENSG00000258654	ENST00000556397.1	TSL:4	n.245-6466C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 56180 AN: 132980 Hom.: 2114 Cov.: 98

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.424

GnomAD4 exome AF: 0.402 AC: 1818 AN: 4526 Hom.: 93 Cov.: 0 AF XY: 0.400 AC XY: 1354 AN XY: 3384

African (AFR) AF: 0.300 AC: 24 AN: 80

American (AMR) AF: 0.316 AC: 12 AN: 38

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 9 AN: 22

East Asian (EAS) AF: 0.0705 AC: 11 AN: 156

South Asian (SAS) AF: 0.336 AC: 43 AN: 128

European-Finnish (FIN) AF: 0.445 AC: 113 AN: 254

Middle Eastern (MID) AF: 0.423 AC: 22 AN: 52

European-Non Finnish (NFE) AF: 0.422 AC: 1460 AN: 3462

Other (OTH) AF: 0.371 AC: 124 AN: 334

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.422 AC: 56177 AN: 133062 Hom.: 2117 Cov.: 98 AF XY: 0.417 AC XY: 27037 AN XY: 64766

African (AFR) AF: 0.381 AC: 13009 AN: 34172

American (AMR) AF: 0.390 AC: 5217 AN: 13390

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1533 AN: 3204

East Asian (EAS) AF: 0.181 AC: 719 AN: 3972

South Asian (SAS) AF: 0.366 AC: 1527 AN: 4176

European-Finnish (FIN) AF: 0.428 AC: 4026 AN: 9414

Middle Eastern (MID) AF: 0.511 AC: 135 AN: 264

European-Non Finnish (NFE) AF: 0.467 AC: 28820 AN: 61746

Other (OTH) AF: 0.418 AC: 789 AN: 1888

Alfa AF: 0.315 Hom.: 86

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.31
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1039353;

hg19: chr15-20557661;