ENST00000790166.1:n.253-6372C>T

Variant names:

• chr1-107035210-G-A
• rs4118325
• ENST00000790166.1:n.253-6372C>T

Variant summary

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

The ENST00000790166.1(ENSG00000302874):​n.253-6372C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,890 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: ENSG00000302874 ENST00000790166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 33 publications found

Genes affected

ENSG00000302874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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
ENSG00000302874	ENST00000790166.1	n.253-6372C>T		intron_variant	Intron 1 of 2
ENSG00000302874	ENST00000790167.1	n.261+2613C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31906 AN: 151772 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.210 AC: 31933 AN: 151890 Hom.: 3386 Cov.: 32 AF XY: 0.213 AC XY: 15817 AN XY: 74220

African (AFR) AF: 0.249 AC: 10292 AN: 41384

American (AMR) AF: 0.184 AC: 2810 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.154 AC: 795 AN: 5164

South Asian (SAS) AF: 0.201 AC: 967 AN: 4810

European-Finnish (FIN) AF: 0.253 AC: 2669 AN: 10542

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13076 AN: 67956

Other (OTH) AF: 0.216 AC: 455 AN: 2106

Alfa AF: 0.190 Hom.: 11812

Bravo AF: 0.203

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4118325; hg19: chr1-107577832;