rs4815683

Variant names:

• chr20-4280002-A-C
• rs4815683
• ENST00000755410.1:n.50+37240A>C

Variant summary

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

The ENST00000755410.1(ENSG00000298420):​n.50+37240A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,168 control chromosomes in the GnomAD database, including 2,702 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 0.18 (2702 hom., cov: 32)
• Consequence: ENSG00000298420 ENST00000755410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 2 publications found

Genes affected

ENSG00000298420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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
ENSG00000298420	ENST00000755410.1	n.50+37240A>C		intron_variant	Intron 1 of 3
ENSG00000298420	ENST00000755411.1	n.554+17889A>C		intron_variant	Intron 1 of 2
ENSG00000298420	ENST00000755412.1	n.74-15020A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26661 AN: 152050 Hom.: 2701 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.175 AC: 26669 AN: 152168 Hom.: 2702 Cov.: 32 AF XY: 0.173 AC XY: 12836 AN XY: 74406

African (AFR) AF: 0.109 AC: 4537 AN: 41542

American (AMR) AF: 0.143 AC: 2181 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.140 AC: 674 AN: 4814

European-Finnish (FIN) AF: 0.232 AC: 2451 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15427 AN: 67968

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.211 Hom.: 5947

Bravo AF: 0.165

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.48
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4815683; hg19: chr20-4260649;