5-28747216-G-C

Variant summary

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

The ENST00000653909.1(ENSG00000250453):n.322-37242C>G 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 0.567 in 151,904 control chromosomes in the GnomAD database, including 24,882 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 0.57 (24882 hom., cov: 32)
• Consequence: ENST00000653909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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 (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986409	XR_001742621.1	n.182+3047G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653909.1	n.322-37242C>G		intron_variant, non_coding_transcript_variant
	ENST00000660682.1	n.337-37242C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86102 AN: 151786 Hom.: 24883 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86142 AN: 151904 Hom.: 24882 Cov.: 32 AF XY: 0.573 AC XY: 42521 AN XY: 74230

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.584

Alfa AF: 0.587 Hom.: 13286

Bravo AF: 0.567

Asia WGS AF: 0.624 AC: 2171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.080
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2548003; hg19: chr5-28747323;