chr20-39552181-C-T

Variant names:

• chr20-39552181-C-T
• rs2024791
• ENST00000774323.1:n.210-4609C>T

Variant summary

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

The ENST00000774323.1(ENSG00000300834):​n.210-4609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,228 control chromosomes in the GnomAD database, including 207 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 0.043 (207 hom., cov: 32)
• Consequence: ENSG00000300834 ENST00000774323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906
• Publications: 0 publications found

Genes affected

ENSG00000300834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774323.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300834	ENST00000774323.1		n.210-4609C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0427 AC: 6499 AN: 152110 Hom.: 205 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0428 AC: 6508 AN: 152228 Hom.: 207 Cov.: 32 AF XY: 0.0424 AC XY: 3154 AN XY: 74416

African (AFR) AF: 0.0110 AC: 456 AN: 41552

American (AMR) AF: 0.0860 AC: 1316 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5152

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4824

European-Finnish (FIN) AF: 0.0316 AC: 335 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0589 AC: 4006 AN: 68010

Other (OTH) AF: 0.0299 AC: 63 AN: 2108

Alfa AF: 0.0180 Hom.: 95

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs2024791; hg19: chr20-38180824;