ENST00000490856.5:n.108+8189T>C

Variant names:

• chr7-106724153-A-G
• rs342286
• ENST00000490856.5:n.108+8189T>C

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.108+8189T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,042 control chromosomes in the GnomAD database, including 9,985 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 0.33 (9985 hom., cov: 31)
• Consequence: ENSG00000243797 ENST00000490856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 11 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 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
ENSG00000243797	ENST00000490856.5	n.108+8189T>C		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.172+36413T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50602 AN: 151924 Hom.: 9982 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.333 AC: 50608 AN: 152042 Hom.: 9985 Cov.: 31 AF XY: 0.334 AC XY: 24799 AN XY: 74298

African (AFR) AF: 0.122 AC: 5067 AN: 41528

American (AMR) AF: 0.333 AC: 5087 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1234 AN: 5162

South Asian (SAS) AF: 0.356 AC: 1711 AN: 4810

European-Finnish (FIN) AF: 0.455 AC: 4800 AN: 10542

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30077 AN: 67940

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.229 Hom.: 1646

Bravo AF: 0.312

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.76
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs342286; hg19: chr7-106364599;