4-59621517-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000249392 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000249392	ENST00000504537.1	n.114+8694T>C		intron_variant	Intron 1 of 5	3

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

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.644

Alfa AF: 0.684 Hom.: 16135

Bravo AF: 0.635

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6828465; hg19: chr4-60487235;