5-56537692-G-T

Variant names:

• chr5-56537692-G-T
• rs30360
• ENST00000431789.1:n.135C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000234553 (HGNC:):

C5orf67 (HGNC:51252): (chromosome 5 putative open reading frame 67)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431789.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	NR_161255.1		n.283-2464C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234553	ENST00000431789.1	TSL:4	n.135C>A		non_coding_transcript_exon	Exon 1 of 2
	C5orf67	ENST00000611197.2	TSL:5	n.145-2464C>A		intron	N/A
	C5orf67	ENST00000648716.1		n.259-2464C>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.694 AC: 105488 AN: 152060 Hom.: 36571 Cov.: 32 AF XY: 0.695 AC XY: 51623 AN XY: 74324

African (AFR) AF: 0.676 AC: 28047 AN: 41460

American (AMR) AF: 0.704 AC: 10763 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3069 AN: 5164

South Asian (SAS) AF: 0.665 AC: 3204 AN: 4820

European-Finnish (FIN) AF: 0.686 AC: 7242 AN: 10556

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.712 AC: 48413 AN: 67992

Other (OTH) AF: 0.669 AC: 1408 AN: 2106

Alfa AF: 0.702 Hom.: 162640

Bravo AF: 0.693

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.0070

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs30360;

hg19: chr5-55833519;

COSMIC: COSV71157758;

COSMIC: COSV71157758;