5-159392607-C-G

Position:

• chr5-159392607-C-G

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+30C>G 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 0.323 in 152,066 control chromosomes in the GnomAD database, including 8,051 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 0.32 (8051 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENST00000635333.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000635333.1	n.327+30C>G		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.533-23917C>G		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.54-23917C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49109 AN: 151938 Hom.: 8046 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.323 AC: 49139 AN: 152056 Hom.: 8051 Cov.: 32 AF XY: 0.323 AC XY: 24048 AN XY: 74350

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.340

Alfa AF: 0.308 Hom.: 885

Bravo AF: 0.326

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6861600; hg19: chr5-158819615;