chr5-31532322-A-T

Position:

• chr5-31532322-A-T

Variant summary

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

The NM_018356.3(C5orf22):​c.-71A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.98 in 1,531,754 control chromosomes in the GnomAD database, including 736,551 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 0.98 (72990 hom., cov: 31)
  • Exomes 𝑓: 0.98 (663561 hom.)
• Consequence: C5orf22 NM_018356.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

Genes affected

C5orf22 (HGNC:25639): (chromosome 5 open reading frame 22)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf22	NM_018356.3	c.-71A>T		5_prime_UTR_variant	1/9	ENST00000325366.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf22	ENST00000325366.14	c.-71A>T		5_prime_UTR_variant	1/9	1	NM_018356.3	P1

Frequencies

GnomAD3 genomes AF: 0.979 AC: 148814 AN: 152054 Hom.: 72935 Cov.: 31

Gnomad AFR AF: 0.998

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.978

GnomAD4 exome AF: 0.980 AC: 1351962 AN: 1379582 Hom.: 663561 Cov.: 21 AF XY: 0.979 AC XY: 676355 AN XY: 690722

Gnomad4 AFR exome AF: 0.998

Gnomad4 AMR exome AF: 0.944

Gnomad4 ASJ exome AF: 0.996

Gnomad4 EAS exome AF: 0.785

Gnomad4 SAS exome AF: 0.951

Gnomad4 FIN exome AF: 0.928

Gnomad4 NFE exome AF: 0.993

Gnomad4 OTH exome AF: 0.975

GnomAD4 genome AF: 0.979 AC: 148926 AN: 152172 Hom.: 72990 Cov.: 31 AF XY: 0.974 AC XY: 72468 AN XY: 74380

Gnomad4 AFR AF: 0.998

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.977

Alfa AF: 0.984 Hom.: 8612

Bravo AF: 0.981

Asia WGS AF: 0.894 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2291109; hg19: chr5-31532429;