ENST00000727174.1:n.342+11354G>A

Variant names:

• chr20-48551929-C-T
• rs4810813
• ENST00000727174.1:n.342+11354G>A

Variant summary

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

The ENST00000727174.1(ENSG00000294979):​n.342+11354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,876 control chromosomes in the GnomAD database, including 33,143 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 (33143 hom., cov: 31)
• Consequence: ENSG00000294979 ENST00000727174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372646	XR_936817.4	n.343-7594G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294979	ENST00000727174.1	n.342+11354G>A		intron_variant	Intron 1 of 2
ENSG00000294979	ENST00000727175.1	n.340-7594G>A		intron_variant	Intron 1 of 3
ENSG00000294979	ENST00000727176.1	n.343-7594G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99274 AN: 151758 Hom.: 33095 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.654 AC: 99378 AN: 151876 Hom.: 33143 Cov.: 31 AF XY: 0.656 AC XY: 48692 AN XY: 74186

African (AFR) AF: 0.529 AC: 21882 AN: 41374

American (AMR) AF: 0.735 AC: 11215 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2414 AN: 3464

East Asian (EAS) AF: 0.626 AC: 3215 AN: 5132

South Asian (SAS) AF: 0.544 AC: 2615 AN: 4810

European-Finnish (FIN) AF: 0.759 AC: 8009 AN: 10550

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

European-Non Finnish (NFE) AF: 0.703 AC: 47773 AN: 67970

Other (OTH) AF: 0.651 AC: 1372 AN: 2108

Alfa AF: 0.671 Hom.: 11560

Bravo AF: 0.652

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4810813; hg19: chr20-47168467;