20-23509041-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000260202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000260202	ENST00000619495.1	n.438+9576G>A		intron_variant	Intron 1 of 1	4

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.355

Alfa AF: 0.402 Hom.: 6256

Bravo AF: 0.331

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3004119; hg19: chr20-23489678;