rs1511453

Positions:

• chr4-23586839-G-A

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.117+25800G>A 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 0.0929 in 152,064 control chromosomes in the GnomAD database, including 797 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 0.093 (797 hom., cov: 33)
• Consequence: ENST00000514290.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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 (EAS) allele frequency at 95% confidence interval = 0.194 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
	ENST00000514290.1	n.117+25800G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14106 AN: 151944 Hom.: 791 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0929 AC: 14120 AN: 152064 Hom.: 797 Cov.: 33 AF XY: 0.0948 AC XY: 7043 AN XY: 74326

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0910

Alfa AF: 0.0898 Hom.: 357

Bravo AF: 0.103

Asia WGS AF: 0.123 AC: 426 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	0.18
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1511453; hg19: chr4-23588462;