4-59575004-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000249392 (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 (AMR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249392	ENST00000504537.1	TSL:3	n.175-646C>T		intron	N/A

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

African (AFR) AF: 0.117 AC: 4852 AN: 41460

American (AMR) AF: 0.357 AC: 5420 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 725 AN: 3456

East Asian (EAS) AF: 0.136 AC: 700 AN: 5156

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2707 AN: 10554

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18692 AN: 67666

Other (OTH) AF: 0.251 AC: 529 AN: 2106

Alfa AF: 0.273 Hom.: 2349

Bravo AF: 0.234

Asia WGS AF: 0.213 AC: 738 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.37
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1486307; hg19: chr4-60440722;