20-23509041-C-T

Variant names:

• chr20-23509041-C-T
• rs3004119
• ENST00000619495.1:n.438+9576G>A

Variant summary

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

The ENST00000619495.1(ENSG00000260202):​n.438+9576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,032 control chromosomes in the GnomAD database, including 10,930 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 0.35 (10930 hom., cov: 33)
• Consequence: ENSG00000260202 ENST00000619495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 4 publications found

Genes affected

ENSG00000260202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619495.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260202	ENST00000619495.1	TSL:4	n.438+9576G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53248 AN: 151912 Hom.: 10927 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.350 AC: 53249 AN: 152032 Hom.: 10930 Cov.: 33 AF XY: 0.350 AC XY: 26015 AN XY: 74278

African (AFR) AF: 0.133 AC: 5536 AN: 41470

American (AMR) AF: 0.386 AC: 5908 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3466

East Asian (EAS) AF: 0.227 AC: 1172 AN: 5156

South Asian (SAS) AF: 0.378 AC: 1821 AN: 4812

European-Finnish (FIN) AF: 0.504 AC: 5319 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30849 AN: 67966

Other (OTH) AF: 0.355 AC: 747 AN: 2106

Alfa AF: 0.399 Hom.: 9077

Bravo AF: 0.331

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.17
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3004119; hg19: chr20-23489678;