chr4-6205057-G-A

Position:

• chr4-6205057-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507424.1(ENSG00000251408):​n.2529G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,092 control chromosomes in the GnomAD database, including 21,149 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 0.52 (21136 hom., cov: 31)
  • Exomes 𝑓: 0.56 (13 hom.)
• Consequence: ENST00000507424.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP1-DT	NR_037863.1	n.207+4118G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000507424.1	n.2529G>A		non_coding_transcript_exon_variant	2/2	2
	ENST00000508601.2	n.207+4118G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78977 AN: 151880 Hom.: 21133 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.564 AC: 53 AN: 94 Hom.: 13 Cov.: 0 AF XY: 0.569 AC XY: 41 AN XY: 72

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.875

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.520 AC: 79015 AN: 151998 Hom.: 21136 Cov.: 31 AF XY: 0.517 AC XY: 38417 AN XY: 74282

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.540

Alfa AF: 0.582 Hom.: 6447

Bravo AF: 0.509

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10003892; hg19: chr4-6206784;