NM_005191.4:c.*214T>G

Variant names:

• chr3-119525574-A-C
• rs7628626
• NM_005191.4:c.*214T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005191.4. 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
	CD80	NM_005191.4	MANE Select	c.*214T>G		3_prime_UTR	Exon 7 of 7	NP_005182.1	P33681-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD80	ENST00000264246.8	TSL:1 MANE Select	c.*214T>G		3_prime_UTR	Exon 7 of 7	ENSP00000264246.3	P33681-1
	CD80	ENST00000853991.1		c.*214T>G		3_prime_UTR	Exon 8 of 8	ENSP00000524050.1
	CD80	ENST00000853992.1		c.*214T>G		3_prime_UTR	Exon 6 of 6	ENSP00000524051.1

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

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 0.896 AC: 310 AN: 346

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.929 AC: 13 AN: 14

Other (OTH) AF: 1.00 AC: 4 AN: 4

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

African (AFR) AF: 0.829 AC: 34386 AN: 41458

American (AMR) AF: 0.778 AC: 11845 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2531 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4495 AN: 5172

South Asian (SAS) AF: 0.863 AC: 4164 AN: 4826

European-Finnish (FIN) AF: 0.865 AC: 9122 AN: 10550

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55824 AN: 67970

Other (OTH) AF: 0.814 AC: 1715 AN: 2106

Alfa AF: 0.816 Hom.: 199272

Bravo AF: 0.815

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

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

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

Other links and lift over

dbSNP: rs7628626;

hg19: chr3-119244421;