20-2477514-T-C

Position:

• chr20-2477514-T-C

Variant summary

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

The ENST00000461548.1(ENSG00000256566):​n.305-9756A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,094 control chromosomes in the GnomAD database, including 49,230 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 0.80 (49230 hom., cov: 32)
• Consequence: ENSG00000256566 ENST00000461548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

ENSG00000256566 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2477514T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256566	ENST00000461548.1	n.305-9756A>G		intron_variant		5		ENSP00000456213.1

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121187 AN: 151976 Hom.: 49218 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.797 AC: 121240 AN: 152094 Hom.: 49230 Cov.: 32 AF XY: 0.798 AC XY: 59340 AN XY: 74348

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.820

Alfa AF: 0.837 Hom.: 23998

Bravo AF: 0.795

Asia WGS AF: 0.865 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815266; hg19: chr20-2458160;