5-1252835-T-C

Variant names:

• chr5-1252835-T-C
• rs2853691
• ENST00000666708.1:n.288+542T>C

Variant summary

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

The ENST00000666708.1(ENSG00000287486):​n.288+542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 129,358 control chromosomes in the GnomAD database, including 11,966 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 0.45 (11966 hom., cov: 25)
• Consequence: ENSG00000287486 ENST00000666708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 16 publications found

Genes affected

ENSG00000287486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666708.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287486	ENST00000666708.1		n.288+542T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.450 AC: 58196 AN: 129262 Hom.: 11948 Cov.: 25

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.450 AC: 58256 AN: 129358 Hom.: 11966 Cov.: 25 AF XY: 0.453 AC XY: 28082 AN XY: 62048

African (AFR) AF: 0.586 AC: 21836 AN: 37248

American (AMR) AF: 0.460 AC: 5566 AN: 12090

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 894 AN: 2954

East Asian (EAS) AF: 0.325 AC: 1288 AN: 3964

South Asian (SAS) AF: 0.482 AC: 1915 AN: 3974

European-Finnish (FIN) AF: 0.400 AC: 2807 AN: 7026

Middle Eastern (MID) AF: 0.382 AC: 84 AN: 220

European-Non Finnish (NFE) AF: 0.385 AC: 22896 AN: 59400

Other (OTH) AF: 0.412 AC: 706 AN: 1712

Alfa AF: 0.219 Hom.: 455

Bravo AF: 0.399

Asia WGS AF: 0.350 AC: 1217 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.55
DANN	Benign	0.077
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2853691; hg19: chr5-1252950;