chr4-59566236-T-G

Variant names:

• chr4-59566236-T-G
• rs10517468
• ENST00000504537.1:n.236-1891A>C

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.236-1891A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,158 control chromosomes in the GnomAD database, including 4,482 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 (4482 hom., cov: 32)
• Consequence: ENSG00000249392 ENST00000504537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.347 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249392	ENST00000504537.1	TSL:3	n.236-1891A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34724 AN: 152038 Hom.: 4476 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.228 AC: 34736 AN: 152158 Hom.: 4482 Cov.: 32 AF XY: 0.230 AC XY: 17098 AN XY: 74388

African (AFR) AF: 0.116 AC: 4806 AN: 41518

American (AMR) AF: 0.355 AC: 5422 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3468

East Asian (EAS) AF: 0.136 AC: 702 AN: 5180

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4828

European-Finnish (FIN) AF: 0.247 AC: 2611 AN: 10588

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18460 AN: 67980

Other (OTH) AF: 0.246 AC: 520 AN: 2110

Alfa AF: 0.247 Hom.: 9504

Bravo AF: 0.231

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10517468;

hg19: chr4-60431954;