rs7630595

Variant names:

• chr3-119538392-G-A
• rs7630595
• NM_005191.4:c.419-974C>T

Variant summary

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

The NM_005191.4(CD80):​c.419-974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 151,958 control chromosomes in the GnomAD database, including 770 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 0.088 (770 hom., cov: 32)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD80	NM_005191.4	c.419-974C>T		intron_variant	Intron 3 of 6	ENST00000264246.8	NP_005182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD80	ENST00000264246.8	c.419-974C>T		intron_variant	Intron 3 of 6	1	NM_005191.4	ENSP00000264246.3
CD80	ENST00000478182.5	c.419-974C>T		intron_variant	Intron 3 of 5	1		ENSP00000418364.1
CD80	ENST00000383669.3	c.419-974C>T		intron_variant	Intron 2 of 3	1		ENSP00000373165.3

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13375 AN: 151840 Hom.: 770 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0901

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

GnomAD4 genome AF: 0.0880 AC: 13371 AN: 151958 Hom.: 770 Cov.: 32 AF XY: 0.0900 AC XY: 6681 AN XY: 74234

African (AFR) AF: 0.0254 AC: 1052 AN: 41450

American (AMR) AF: 0.0774 AC: 1180 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.000968 AC: 5 AN: 5166

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4810

European-Finnish (FIN) AF: 0.174 AC: 1833 AN: 10510

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8462 AN: 67988

Other (OTH) AF: 0.0892 AC: 188 AN: 2108

Alfa AF: 0.0993 Hom.: 110

Bravo AF: 0.0789

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		0.044
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: rs7630595; hg19: chr3-119257239;