rs297755

Variant names:

• chr20-4521229-G-A
• rs297755
• ENST00000419863.1:n.42-3845G>A

Variant summary

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

The ENST00000419863.1(ENSG00000238282):​n.42-3845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,976 control chromosomes in the GnomAD database, including 39,662 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 0.70 (39662 hom., cov: 31)
• Consequence: ENSG00000238282 ENST00000419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 2 publications found

Genes affected

ENSG00000238282 (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 (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238282	ENST00000419863.1	n.42-3845G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106879 AN: 151860 Hom.: 39648 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.704 AC: 106941 AN: 151976 Hom.: 39662 Cov.: 31 AF XY: 0.704 AC XY: 52271 AN XY: 74252

African (AFR) AF: 0.498 AC: 20623 AN: 41442

American (AMR) AF: 0.759 AC: 11604 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2858 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1598 AN: 5126

South Asian (SAS) AF: 0.610 AC: 2929 AN: 4802

European-Finnish (FIN) AF: 0.870 AC: 9216 AN: 10592

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55659 AN: 67944

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.767 Hom.: 5709

Bravo AF: 0.685

Asia WGS AF: 0.479 AC: 1672 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	1.8
DANN	Benign	0.79
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs297755; hg19: chr20-4501875;