rs398655

Positions:

• chr13-33013514-A-C
• chr13-33013514-A-G
• chr13-33013514-A-T

Variant summary

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

The XR_007063749.1(LOC124903151):​n.339T>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 0.512 in 152,000 control chromosomes in the GnomAD database, including 20,741 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 0.51 (20741 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC124903151 XR_007063749.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

Genes affected

LOC124903151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903151	XR_007063749.1	n.339T>G		non_coding_transcript_exon_variant	2/2
LOC124903151	XM_047430819.1	c.729T>G	p.His243Gln	missense_variant	2/2		XP_047286775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77678 AN: 151884 Hom.: 20705 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.486

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: 0.512 AC: 77756 AN: 152000 Hom.: 20741 Cov.: 32 AF XY: 0.516 AC XY: 38354 AN XY: 74290

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.481

Alfa AF: 0.440 Hom.: 23755

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.086
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs398655; hg19: chr13-33587652;