chr5-1252835-T-C

Position:

• chr5-1252835-T-C

Variant summary

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

The ENST00000666708.1(ENSG00000287486):​n.288+542T>C variant causes a intron, non coding transcript 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: ENST00000666708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666708.1	n.288+542T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.412

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853691; hg19: chr5-1252950;