chr3-119525574-A-C

Position:

• chr3-119525574-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_005191.4(CD80):​c.*214T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,346 control chromosomes in the GnomAD database, including 51,707 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.82 (51558 hom., cov: 30)
  • Exomes 𝑓: 0.90 (149 hom.)
• Consequence: CD80 NM_005191.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.638

Genes affected

CD80 (HGNC:1700): (CD80 molecule) The protein encoded by this gene is a membrane receptor that is activated by the binding of CD28 or CTLA-4. The activated protein induces T-cell proliferation and cytokine production. This protein can act as a receptor for adenovirus subgroup B and may play a role in lupus neuropathy. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 3-119525574-A-C is Benign according to our data. Variant chr3-119525574-A-C is described in ClinVar as [Benign]. Clinvar id is 1224718.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD80	NM_005191.4	c.*214T>G		3_prime_UTR_variant	7/7	ENST00000264246.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD80	ENST00000264246.8	c.*214T>G		3_prime_UTR_variant	7/7	1	NM_005191.4	P2

Frequencies

GnomAD3 genomes AF: 0.823 AC: 124984 AN: 151860 Hom.: 51516 Cov.: 30

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.815

GnomAD4 exome AF: 0.899 AC: 329 AN: 366 Hom.: 149 Cov.: 0 AF XY: 0.893 AC XY: 200 AN XY: 224

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.896

Gnomad4 NFE exome AF: 0.929

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.823 AC: 125085 AN: 151980 Hom.: 51558 Cov.: 30 AF XY: 0.825 AC XY: 61256 AN XY: 74292

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.814

Alfa AF: 0.812 Hom.: 84729

Bravo AF: 0.815

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 2020	This variant is associated with the following publications: (PMID: 25497975) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs7628626; hg19: chr3-119244421;