5-25972712-C-T

Position:

• chr5-25972712-C-T

Variant summary

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

The ENST00000658114.1(ENSG00000286625):​n.112+8762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,664 control chromosomes in the GnomAD database, including 7,403 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 (7403 hom., cov: 33)
• Consequence: ENSG00000286625 ENST00000658114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

Genes affected

ENSG00000286625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901176	XR_007059127.1	n.58+8762C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286625	ENST00000658114.1	n.112+8762C>T		intron_variant
ENSG00000286625	ENST00000668718.1	n.49+8762C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42336 AN: 151548 Hom.: 7402 Cov.: 33

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42346 AN: 151664 Hom.: 7403 Cov.: 33 AF XY: 0.281 AC XY: 20856 AN XY: 74108

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.307

Alfa AF: 0.355 Hom.: 13150

Bravo AF: 0.260

Asia WGS AF: 0.241 AC: 836 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4327572; hg19: chr5-25972821;