rs297765

Variant names:

• chr20-4506463-A-G
• rs297765
• ENST00000419863.1:n.42-18611A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-4506463-A-G
• chr20-4506463-A-T

Variant summary

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

The ENST00000419863.1(ENSG00000238282):​n.42-18611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,000 control chromosomes in the GnomAD database, including 40,542 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 0.73 (40542 hom., cov: 30)
• Consequence: ENSG00000238282 ENST00000419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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.42-18611A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110147 AN: 151882 Hom.: 40506 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.725 AC: 110249 AN: 152000 Hom.: 40542 Cov.: 30 AF XY: 0.725 AC XY: 53911 AN XY: 74316

African (AFR) AF: 0.681 AC: 28239 AN: 41444

American (AMR) AF: 0.736 AC: 11250 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2670 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2014 AN: 5158

South Asian (SAS) AF: 0.537 AC: 2582 AN: 4812

European-Finnish (FIN) AF: 0.850 AC: 8989 AN: 10572

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52138 AN: 67946

Other (OTH) AF: 0.743 AC: 1567 AN: 2108

Alfa AF: 0.747 Hom.: 137074

Bravo AF: 0.715

Asia WGS AF: 0.484 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs297765; hg19: chr20-4487111;