3-119550821-G-T

Variant names:

• chr3-119550821-G-T
• rs6808536
• NM_005191.4:c.101-5954C>A

Variant summary

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

The NM_005191.4(CD80):​c.101-5954C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 145,100 control chromosomes in the GnomAD database, including 1,156 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 0.11 (1156 hom., cov: 31)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 10 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD80	NM_005191.4	c.101-5954C>A		intron_variant	Intron 2 of 6	ENST00000264246.8	NP_005182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD80	ENST00000264246.8	c.101-5954C>A		intron_variant	Intron 2 of 6	1	NM_005191.4	ENSP00000264246.3
CD80	ENST00000478182.5	c.101-5954C>A		intron_variant	Intron 2 of 5	1		ENSP00000418364.1
CD80	ENST00000383669.3	c.101-5954C>A		intron_variant	Intron 1 of 3	1		ENSP00000373165.3
CD80	ENST00000463729.1	n.213-5954C>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 16560 AN: 144984 Hom.: 1156 Cov.: 31

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0580

Gnomad AMR AF: 0.0897

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00126

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0608

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.114 AC: 16556 AN: 145100 Hom.: 1156 Cov.: 31 AF XY: 0.114 AC XY: 8108 AN XY: 70964

African (AFR) AF: 0.0319 AC: 1242 AN: 38906

American (AMR) AF: 0.0896 AC: 1309 AN: 14610

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 378 AN: 3348

East Asian (EAS) AF: 0.00126 AC: 6 AN: 4750

South Asian (SAS) AF: 0.0583 AC: 267 AN: 4578

European-Finnish (FIN) AF: 0.201 AC: 2077 AN: 10312

Middle Eastern (MID) AF: 0.0580 AC: 16 AN: 276

European-Non Finnish (NFE) AF: 0.168 AC: 10996 AN: 65462

Other (OTH) AF: 0.108 AC: 215 AN: 1996

Alfa AF: 0.0928 Hom.: 266

Bravo AF: 0.0977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.21
DANN	Benign	0.68
PhyloP100		-1.8
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: rs6808536; hg19: chr3-119269668;