chr14-60240828-C-A

Variant names:

• chr14-60240828-C-A
• rs11628628
• ENST00000532515.1:n.2152G>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000254718 ENST00000532515.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

ENSG00000254718 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927702	NR_188027.1	n.201-374G>T		intron_variant	Intron 2 of 2
LOC101927702	NR_188028.1	n.280-374G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254718	ENST00000532515.1	n.2152G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000254718	ENST00000529171.5	n.235-374G>T		intron_variant	Intron 2 of 2	3
ENSG00000254718	ENST00000553269.6	n.283-374G>T		intron_variant	Intron 2 of 2	3

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.571 AC: 23685 AN: 41492

American (AMR) AF: 0.273 AC: 4176 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3468

East Asian (EAS) AF: 0.152 AC: 788 AN: 5188

South Asian (SAS) AF: 0.450 AC: 2168 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10550

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19965 AN: 67986

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.323 Hom.: 2222

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
PhyloP100		-0.41

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;