5-87097268-A-C

Position:

• chr5-87097268-A-C

Variant summary

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

The ENST00000503349.1(ENSG00000249061):​n.220-8147A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 152,178 control chromosomes in the GnomAD database, including 266 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 0.049 (266 hom., cov: 32)
• Consequence: ENSG00000249061 ENST00000503349.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

Genes affected

ENSG00000249061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4280HG	NR_186582.1	n.375+24553T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249061	ENST00000503349.1	n.220-8147A>C		intron_variant		2
MIR4280HG	ENST00000662995.1	n.287-30488T>G		intron_variant
MIR4280HG	ENST00000666497.1	n.327+24553T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7407 AN: 152060 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0487 AC: 7405 AN: 152178 Hom.: 266 Cov.: 32 AF XY: 0.0468 AC XY: 3478 AN XY: 74394

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.0309

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0654 Hom.: 64

Bravo AF: 0.0443

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62367737; hg19: chr5-86393085;