chr4-59623792-A-G

Variant names:

• chr4-59623792-A-G
• rs6842739
• ENST00000504537.1:n.114+6419T>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+6419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,002 control chromosomes in the GnomAD database, including 31,558 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 (31558 hom., cov: 32)
• Consequence: ENSG00000249392 ENST00000504537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• 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=-0.93).
• 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249392	ENST00000504537.1	TSL:3	n.114+6419T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96723 AN: 151884 Hom.: 31544 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.637 AC: 96771 AN: 152002 Hom.: 31558 Cov.: 32 AF XY: 0.636 AC XY: 47242 AN XY: 74284

African (AFR) AF: 0.484 AC: 20058 AN: 41442

American (AMR) AF: 0.713 AC: 10874 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3372 AN: 5154

South Asian (SAS) AF: 0.628 AC: 3029 AN: 4824

European-Finnish (FIN) AF: 0.661 AC: 6983 AN: 10564

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

European-Non Finnish (NFE) AF: 0.705 AC: 47896 AN: 67980

Other (OTH) AF: 0.647 AC: 1362 AN: 2106

Alfa AF: 0.686 Hom.: 154542

Bravo AF: 0.636

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6842739; hg19: chr4-60489510;