chr4-99265219-A-T

Variant names:

• chr4-99265219-A-T
• rs1230025
• ENST00000500358.6:n.3790-21576A>T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-21576A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,184 control chromosomes in the GnomAD database, including 2,910 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 0.18 (2910 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 8 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=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3790-21576A>T		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3790-21576A>T		intron_variant	Intron 4 of 9	1
ENSG00000246090	ENST00000509295.5	n.444+1409A>T		intron_variant	Intron 2 of 5	1
ENSG00000246090	ENST00000506160.1	n.408-13234A>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27977 AN: 152066 Hom.: 2906 Cov.: 33

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.184 AC: 27986 AN: 152184 Hom.: 2910 Cov.: 33 AF XY: 0.189 AC XY: 14040 AN XY: 74402

African (AFR) AF: 0.0910 AC: 3778 AN: 41536

American (AMR) AF: 0.195 AC: 2971 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.0892 AC: 463 AN: 5190

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2814 AN: 10586

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

European-Non Finnish (NFE) AF: 0.226 AC: 15355 AN: 67996

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.111 Hom.: 194

Bravo AF: 0.170

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.79
DANN	Benign	0.94
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1230025; hg19: chr4-100186376;