chr5-29249289-G-A

Position:

• chr5-29249289-G-A

Variant summary

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

The ENST00000651494.1(ENSG00000286182):​n.172-7301C>T 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 0.331 in 151,838 control chromosomes in the GnomAD database, including 8,607 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 0.33 (8607 hom., cov: 32)
• Consequence: ENST00000651494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651494.1	n.172-7301C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50195 AN: 151720 Hom.: 8602 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.331 AC: 50221 AN: 151838 Hom.: 8607 Cov.: 32 AF XY: 0.329 AC XY: 24405 AN XY: 74188

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.326

Alfa AF: 0.306 Hom.: 9894

Bravo AF: 0.339

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7717789; hg19: chr5-29249396;