14-60240693-G-A

Variant names:

• chr14-60240693-G-A
• rs8019531
• ENST00000532515.1:n.2287C>T

Variant summary

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

The ENST00000532515.1(ENSG00000254718):​n.2287C>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 0.474 in 152,122 control chromosomes in the GnomAD database, including 21,424 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 0.47 (21424 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000254718 ENST00000532515.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 5 publications found

Genes affected

ENSG00000254718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927702	NR_188027.1	n.201-239C>T		intron_variant	Intron 2 of 2
LOC101927702	NR_188028.1	n.280-239C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254718	ENST00000532515.1	n.2287C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000254718	ENST00000529171.5	n.235-239C>T		intron_variant	Intron 2 of 2	3
ENSG00000254718	ENST00000553269.6	n.283-239C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72070 AN: 151998 Hom.: 21373 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.449

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.474 AC: 72171 AN: 152118 Hom.: 21424 Cov.: 32 AF XY: 0.466 AC XY: 34672 AN XY: 74358

African (AFR) AF: 0.851 AC: 35335 AN: 41536

American (AMR) AF: 0.338 AC: 5169 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3472

East Asian (EAS) AF: 0.182 AC: 942 AN: 5170

South Asian (SAS) AF: 0.477 AC: 2299 AN: 4822

European-Finnish (FIN) AF: 0.275 AC: 2904 AN: 10550

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22717 AN: 67948

Other (OTH) AF: 0.445 AC: 942 AN: 2116

Alfa AF: 0.387 Hom.: 4908

Bravo AF: 0.491

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.76
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs8019531; hg19: chr14-60707411;