rs17583753

Variant names:

• chr4-99264507-G-A
• rs17583753
• ENST00000500358.6:n.3790-22288G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-99264507-G-A
• chr4-99264507-G-C
• chr4-99264507-G-T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-22288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,228 control chromosomes in the GnomAD database, including 990 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 0.097 (990 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3790-22288G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3790-22288G>A		intron_variant	Intron 4 of 9	1
ENSG00000246090	ENST00000509295.5	n.444+697G>A		intron_variant	Intron 2 of 5	1
ENSG00000246090	ENST00000506160.1	n.408-13946G>A		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14783 AN: 152110 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0971 AC: 14786 AN: 152228 Hom.: 990 Cov.: 32 AF XY: 0.0956 AC XY: 7113 AN XY: 74398

African (AFR) AF: 0.0229 AC: 953 AN: 41566

American (AMR) AF: 0.0965 AC: 1475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4822

European-Finnish (FIN) AF: 0.162 AC: 1718 AN: 10586

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9456 AN: 68002

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.113 Hom.: 558

Bravo AF: 0.0900

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs17583753; hg19: chr4-100185664;