rs1486307

Variant names:

• chr4-59575004-G-A
• rs1486307
• ENST00000504537.1:n.175-646C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504537.1(ENSG00000249392):​n.175-646C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,584 control chromosomes in the GnomAD database, including 4,574 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 0.23 (4574 hom., cov: 32)
• Consequence: ENSG00000249392 ENST00000504537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

ENSG00000249392 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 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
ENSG00000249392	ENST00000504537.1	n.175-646C>T		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35100 AN: 151464 Hom.: 4568 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.232 AC: 35112 AN: 151584 Hom.: 4574 Cov.: 32 AF XY: 0.233 AC XY: 17280 AN XY: 74080

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.251

Alfa AF: 0.278 Hom.: 1957

Bravo AF: 0.234

Asia WGS AF: 0.213 AC: 738 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486307; hg19: chr4-60440722;