rs1486307

Positions:

• chr4-59575004-G-A

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.175-646C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,584 control chromosomes in the GnomAD database, including 4,574 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 0.23 (4574 hom., cov: 32)
• Consequence: ENST00000504537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504537.1	n.175-646C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35100 AN: 151464 Hom.: 4568 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.232 AC: 35112 AN: 151584 Hom.: 4574 Cov.: 32 AF XY: 0.233 AC XY: 17280 AN XY: 74080

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.251

Alfa AF: 0.278 Hom.: 1957

Bravo AF: 0.234

Asia WGS AF: 0.213 AC: 738 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486307; hg19: chr4-60440722;