3-119542528-A-C

Variant names:

• chr3-119542528-A-C
• rs7648642
• NM_005191.4:c.418+2022T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005191.4(CD80):​c.418+2022T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,900 control chromosomes in the GnomAD database, including 17,190 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 0.47 (17190 hom., cov: 31)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 17 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 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.418+2022T>G		intron	N/A	NP_005182.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD80	ENST00000264246.8	TSL:1 MANE Select	c.418+2022T>G		intron	N/A	ENSP00000264246.3
	CD80	ENST00000478182.5	TSL:1	c.418+2022T>G		intron	N/A	ENSP00000418364.1
	CD80	ENST00000383669.3	TSL:1	c.418+2022T>G		intron	N/A	ENSP00000373165.3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71960 AN: 151782 Hom.: 17175 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.474 AC: 72025 AN: 151900 Hom.: 17190 Cov.: 31 AF XY: 0.471 AC XY: 34976 AN XY: 74216

African (AFR) AF: 0.506 AC: 20958 AN: 41412

American (AMR) AF: 0.441 AC: 6726 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3466

East Asian (EAS) AF: 0.511 AC: 2635 AN: 5154

South Asian (SAS) AF: 0.420 AC: 2020 AN: 4804

European-Finnish (FIN) AF: 0.434 AC: 4588 AN: 10562

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32323 AN: 67948

Other (OTH) AF: 0.447 AC: 940 AN: 2104

Alfa AF: 0.471 Hom.: 55903

Bravo AF: 0.476

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.32
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

Other links and lift over

dbSNP: rs7648642; hg19: chr3-119261375;