ENST00000805841.1:n.191+566G>T

Variant names:

• chr4-74364585-C-A
• rs3806794
• ENST00000805841.1:n.191+566G>T

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.191+566G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 152,190 control chromosomes in the GnomAD database, including 195 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 0.048 (195 hom., cov: 31)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 9 publications found

Genes affected

ENSG00000304732 (HGNC:58817):

LOC105377276 (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 (EAS) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805841.1. 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
	LOC105377276	NR_188415.1		n.191+566G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.191+566G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7271 AN: 152072 Hom.: 194 Cov.: 31

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0477 AC: 7267 AN: 152190 Hom.: 195 Cov.: 31 AF XY: 0.0483 AC XY: 3590 AN XY: 74396

African (AFR) AF: 0.0490 AC: 2034 AN: 41524

American (AMR) AF: 0.0301 AC: 461 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3470

East Asian (EAS) AF: 0.0950 AC: 492 AN: 5178

South Asian (SAS) AF: 0.0711 AC: 342 AN: 4810

European-Finnish (FIN) AF: 0.0516 AC: 546 AN: 10580

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3041 AN: 68012

Other (OTH) AF: 0.0417 AC: 88 AN: 2110

Alfa AF: 0.0421 Hom.: 266

Bravo AF: 0.0457

Asia WGS AF: 0.0760 AC: 263 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	0.85
DANN	Benign	0.58
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs3806794; hg19: chr4-75230302;