rs13150331

Positions:

• chr4-153678470-A-G
• chr4-153678470-A-T

Variant summary

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

The ENST00000507055.1(ENSG00000250771):​n.212A>G 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 0.367 in 152,106 control chromosomes in the GnomAD database, including 11,723 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 0.37 (11723 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENST00000507055.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100419170	NR_134873.1	n.356-32A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507055.1	n.212A>G		non_coding_transcript_exon_variant	1/1
	ENST00000602666.1	n.356-32A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55735 AN: 151988 Hom.: 11708 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.347

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.367 AC: 55759 AN: 152106 Hom.: 11723 Cov.: 33 AF XY: 0.380 AC XY: 28230 AN XY: 74378

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.350

Alfa AF: 0.405 Hom.: 20360

Bravo AF: 0.359

Asia WGS AF: 0.503 AC: 1749 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13150331; hg19: chr4-154599622;