chr5-159347601-C-G

Position:

• chr5-159347601-C-G

Variant summary

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

The ENST00000515337.1(ENSG00000249738):​n.831C>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 0.112 in 152,112 control chromosomes in the GnomAD database, including 1,114 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 0.11 (1114 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000249738 ENST00000515337.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

Genes affected

ENSG00000249738 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.831C>G		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000515337.1	n.831C>G		non_coding_transcript_exon_variant	3/5	2
ENSG00000249738	ENST00000635333.1	n.160C>G		non_coding_transcript_exon_variant	2/8	5
ENSG00000249738	ENST00000641150.1	n.410C>G		non_coding_transcript_exon_variant	3/5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17018 AN: 151994 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0916

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.128

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.112 AC: 17009 AN: 152112 Hom.: 1114 Cov.: 32 AF XY: 0.108 AC XY: 8021 AN XY: 74362

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0908

Gnomad4 SAS AF: 0.0598

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0520 Hom.: 49

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11747112; hg19: chr5-158774609;