chr5-56537692-G-T

Position:

• chr5-56537692-G-T

Variant summary

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

The ENST00000431789.1(ENSG00000234553):​n.135C>A 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 0.694 in 152,060 control chromosomes in the GnomAD database, including 36,571 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 0.69 (36571 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000234553 ENST00000431789.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

ENSG00000234553 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.283-2464C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234553	ENST00000431789.1	n.135C>A		non_coding_transcript_exon_variant	1/2	4
C5orf67	ENST00000648716.1	n.259-2464C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105406 AN: 151942 Hom.: 36539 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.667

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: 0.694 AC: 105488 AN: 152060 Hom.: 36571 Cov.: 32 AF XY: 0.695 AC XY: 51623 AN XY: 74324

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.669

Alfa AF: 0.702 Hom.: 74970

Bravo AF: 0.693

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs30360; hg19: chr5-55833519; COSMIC: COSV71157758; COSMIC: COSV71157758;