20-48543494-G-C

Variant names:

• chr20-48543494-G-C
• rs2904081
• ENST00000727174.1:n.343-9558C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000727174.1(ENSG00000294979):​n.343-9558C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,942 control chromosomes in the GnomAD database, including 38,877 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 0.71 (38877 hom., cov: 31)
• Consequence: ENSG00000294979 ENST00000727174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 1 publications found

Genes affected

ENSG00000294979 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727174.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294979	ENST00000727174.1		n.343-9558C>G		intron	N/A
	ENSG00000294979	ENST00000727175.1		n.583+598C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108334 AN: 151822 Hom.: 38819 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.714 AC: 108454 AN: 151942 Hom.: 38877 Cov.: 31 AF XY: 0.713 AC XY: 52918 AN XY: 74256

African (AFR) AF: 0.721 AC: 29869 AN: 41430

American (AMR) AF: 0.754 AC: 11516 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3242 AN: 5130

South Asian (SAS) AF: 0.551 AC: 2648 AN: 4808

European-Finnish (FIN) AF: 0.761 AC: 8045 AN: 10570

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48303 AN: 67946

Other (OTH) AF: 0.692 AC: 1465 AN: 2116

Alfa AF: 0.706 Hom.: 4701

Bravo AF: 0.720

Asia WGS AF: 0.635 AC: 2211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.057
DANN	Benign	0.52
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2904081; hg19: chr20-47160032; COSMIC: COSV60104952;