rs4485619

Variant names:

• chr20-11323028-T-C
• rs4485619
• ENST00000784589.1:n.570-9868A>G

Variant summary

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

The ENST00000784589.1(ENSG00000302131):​n.570-9868A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,096 control chromosomes in the GnomAD database, including 4,694 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 0.24 (4694 hom., cov: 32)
• Consequence: ENSG00000302131 ENST00000784589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 publications found

Genes affected

ENSG00000302131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372529	XR_937261.2	n.552-9868A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302131	ENST00000784589.1	n.570-9868A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36744 AN: 151978 Hom.: 4690 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.242 AC: 36771 AN: 152096 Hom.: 4694 Cov.: 32 AF XY: 0.240 AC XY: 17810 AN XY: 74356

African (AFR) AF: 0.192 AC: 7957 AN: 41500

American (AMR) AF: 0.247 AC: 3770 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 938 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2308 AN: 5156

South Asian (SAS) AF: 0.345 AC: 1666 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10598

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17356 AN: 67974

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.256 Hom.: 6624

Bravo AF: 0.248

Asia WGS AF: 0.387 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.52
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs4485619; hg19: chr20-11303676;