rs564041

Variant names:

• chr4-20250644-G-A
• rs564041
• ENST00000815627.1:n.264+1586C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-20250644-G-A
• chr4-20250644-G-C

Variant summary

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

The ENST00000815627.1(ENSG00000306143):​n.264+1586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,028 control chromosomes in the GnomAD database, including 31,918 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 0.64 (31918 hom., cov: 32)
• Consequence: ENSG00000306143 ENST00000815627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 6 publications found

Genes affected

ENSG00000306143 (HGNC:58754):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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
ENSG00000306143	ENST00000815627.1	n.264+1586C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96561 AN: 151910 Hom.: 31920 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.635 AC: 96582 AN: 152028 Hom.: 31918 Cov.: 32 AF XY: 0.639 AC XY: 47506 AN XY: 74304

African (AFR) AF: 0.428 AC: 17745 AN: 41424

American (AMR) AF: 0.717 AC: 10966 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2689 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4175 AN: 5158

South Asian (SAS) AF: 0.693 AC: 3329 AN: 4806

European-Finnish (FIN) AF: 0.681 AC: 7197 AN: 10572

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48133 AN: 67994

Other (OTH) AF: 0.655 AC: 1383 AN: 2110

Alfa AF: 0.689 Hom.: 18844

Bravo AF: 0.632

Asia WGS AF: 0.697 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.78
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs564041; hg19: chr4-20252267;