4-59621517-A-G

Variant names:

• chr4-59621517-A-G
• rs6828465
• ENST00000504537.1:n.114+8694T>C

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.114+8694T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,984 control chromosomes in the GnomAD database, including 31,523 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 (31523 hom., cov: 31)
• Consequence: ENSG00000249392 ENST00000504537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.701 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.114+8694T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96643 AN: 151866 Hom.: 31509 Cov.: 31

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.636 AC: 96692 AN: 151984 Hom.: 31523 Cov.: 31 AF XY: 0.636 AC XY: 47227 AN XY: 74274

African (AFR) AF: 0.484 AC: 20057 AN: 41432

American (AMR) AF: 0.713 AC: 10888 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3468

East Asian (EAS) AF: 0.654 AC: 3363 AN: 5142

South Asian (SAS) AF: 0.629 AC: 3024 AN: 4810

European-Finnish (FIN) AF: 0.662 AC: 6990 AN: 10558

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47818 AN: 67980

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.685 Hom.: 18154

Bravo AF: 0.635

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs6828465; hg19: chr4-60487235;