rs878198

Variant names:

• chr20-48563115-C-A
• rs878198
• ENST00000727174.1:n.342+168G>T

Variant summary

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

The ENST00000727174.1(ENSG00000294979):​n.342+168G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,010 control chromosomes in the GnomAD database, including 32,547 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 0.65 (32547 hom., cov: 32)
• Consequence: ENSG00000294979 ENST00000727174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372646	XR_936817.4	n.342+168G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294979	ENST00000727174.1	n.342+168G>T		intron_variant	Intron 1 of 2
ENSG00000294979	ENST00000727175.1	n.339+168G>T		intron_variant	Intron 1 of 3
ENSG00000294979	ENST00000727176.1	n.342+168G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98036 AN: 151890 Hom.: 32506 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98133 AN: 152010 Hom.: 32547 Cov.: 32 AF XY: 0.649 AC XY: 48240 AN XY: 74312

African (AFR) AF: 0.496 AC: 20569 AN: 41446

American (AMR) AF: 0.730 AC: 11158 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3241 AN: 5174

South Asian (SAS) AF: 0.565 AC: 2721 AN: 4816

European-Finnish (FIN) AF: 0.769 AC: 8136 AN: 10580

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47683 AN: 67936

Other (OTH) AF: 0.636 AC: 1340 AN: 2106

Alfa AF: 0.669 Hom.: 27541

Bravo AF: 0.640

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs878198; hg19: chr20-47179653;