ENST00000805841.1:n.192-3052C>T

Variant names:

• chr4-74333356-G-A
• rs1903256
• ENST00000805841.1:n.192-3052C>T

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.192-3052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 151,968 control chromosomes in the GnomAD database, including 1,098 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 0.099 (1098 hom., cov: 32)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 1 publications found

Genes affected

ENSG00000304732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377276	NR_188415.1	n.192-3052C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304732	ENST00000805841.1	n.192-3052C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14946 AN: 151854 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0986 AC: 14985 AN: 151968 Hom.: 1098 Cov.: 32 AF XY: 0.102 AC XY: 7605 AN XY: 74294

African (AFR) AF: 0.196 AC: 8106 AN: 41428

American (AMR) AF: 0.100 AC: 1533 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.120 AC: 620 AN: 5180

South Asian (SAS) AF: 0.170 AC: 819 AN: 4814

European-Finnish (FIN) AF: 0.0633 AC: 665 AN: 10510

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0430 AC: 2922 AN: 67984

Other (OTH) AF: 0.0886 AC: 187 AN: 2110

Alfa AF: 0.0616 Hom.: 92

Bravo AF: 0.100

Asia WGS AF: 0.167 AC: 581 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.16
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1903256; hg19: chr4-75199073;