ENST00000500358.6:n.4161-3713C>T

Variant names:

• chr4-99296586-C-T
• rs1826909
• ENST00000500358.6:n.4161-3713C>T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.4161-3713C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,936 control chromosomes in the GnomAD database, including 7,367 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 0.29 (7367 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 17 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.4161-3713C>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.4161-3713C>T		intron_variant	Intron 7 of 9	1
ENSG00000246090	ENST00000509939.1	n.71-3713C>T		intron_variant	Intron 1 of 3	3
ENSG00000246090	ENST00000661393.1	n.1269-3713C>T		intron_variant	Intron 7 of 9

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43899 AN: 151818 Hom.: 7368 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.289 AC: 43912 AN: 151936 Hom.: 7367 Cov.: 33 AF XY: 0.282 AC XY: 20931 AN XY: 74250

African (AFR) AF: 0.150 AC: 6234 AN: 41470

American (AMR) AF: 0.270 AC: 4116 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1565 AN: 3462

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5184

South Asian (SAS) AF: 0.151 AC: 726 AN: 4822

European-Finnish (FIN) AF: 0.360 AC: 3789 AN: 10532

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26100 AN: 67884

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.346 Hom.: 29580

Bravo AF: 0.277

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.37
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1826909; hg19: chr4-100217743;