rs11628628

chr14-60240828-C-A

Variant summary

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

The ENST00000532515.1(ENSG00000254718):n.2152G>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 0.367 in 152,124 control chromosomes in the GnomAD database, including 11,600 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 0.37 (11599 hom., cov: 33)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENST00000532515.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927702	XR_001750787.3	n.2135G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000532515.1	n.2152G>T		non_coding_transcript_exon_variant	2/2	1
	ENST00000529171.5	n.235-374G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000553269.5	n.278-374G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000553775.1	n.133-374G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55785 AN: 151994 Hom.: 11579 Cov.: 33

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.250 AC: 3 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.367 AC: 55849 AN: 152112 Hom.: 11599 Cov.: 33 AF XY: 0.361 AC XY: 26867 AN XY: 74344

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.342

Alfa AF: 0.318 Hom.: 2095

Bravo AF: 0.374

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11628628; hg19: chr14-60707546;